The Peloponnesian War (431 to 404 BC) was a testing time for the Athenian judicial system, every victory brought forth new heroes and every loss new scapegoats. The Athenians had lost their strongest asset, the leadership of Pericles, when the plague hit the city in the first year of the war, the lack of an experienced successor and the physical and mental exhaustion of the population from the plague created fertile ground for demagoguery and slander.
Cleon, Pericles' immediate successor, and Demosthenes were regularly lampooned by Aristophanes, and Nicias, although largely responsible for the peace treaty that ended the first part of the war, had little success in battle. Alcibiades rise to prominence during the interlude and the second part of the war is a tale of intense political struggle, and in one way or the other involves all the principals of the trial of the generals. Both Theramenes and Thrasybulus were his allies, the three men had fought side by side in several battles of the war, and were all involved in the coup of 411 BC.
Theramenes was part of the short lived oligarchy of the Four Hundred that followed the coup, and remains an enigmatic and highly controversial figure, but there's little doubt that at the time of the Battle of Arginusae both he and Thrasybulus were extremely influential. Alcibiades alone, who had returned to Athens only a year prior to the Battle of Arginusae, following his defection to Sparta after he was condemned to death in absentia during the ill fated Sicilian Expedition, was an extremely powerful ally and one that had proven in the past that was quite capable of manipulating the assembly in his favour.
Nevertheless, the aftermath of the Battle of Arginusae is atypical, even in the uncertain climate of the later half of an unprecedentedly long war. By Xenophon's account the Athenian victory was quite unexpected, the Athenian fleet was essentially a relief squadron, hastily assembled while the main fleet under Conon was blockaded by the Spartans in Mytilene, in the island of Lesbos:
[Xen. Hell. 1.6.24] When the Athenians heard of what had happened and of the blockade, they voted to go to the rescue with one hundred and ten ships, putting aboard all who were of military age, whether slave or free; and within thirty days they manned the one hundred and ten ships and set forth. Even the knights went aboard in considerable numbers.
A bunch of kids, along with slaves (that were rarely employed in military service, thus were untrained) and knights (who were exempt from service at sea) faced a superior fleet that at the time had little trouble at keeping the main Athenian fleet at bay and delivered a decisive blow. Callicratidas, the Spartan naval commander, was killed when his ship was sunk and the Spartans lost nine of their ships, only one escaped, and sixty ships belonging to their allies.
Our other main source for the events that followed and lead to the trial is Diodorus Siculus', unfortunately Thucydides' History of the Peloponnesian War ends in 411 BC. Xenophon's account is the one the Wikipedia article is primarily based upon, here's what Diodorus had to say:
[Diod. 13.101.1] When the Athenians learned of their success at the Arginusae, they commended the generals for the victory but were incensed that they had allowed the men who had died to maintain their supremacy to go unburied.
[Diod. 13.101.2] Since Theramenes and Thrasybulus had gone off to Athens in advance of the others, the generals, having assumed that it was they who had made accusations before the populace with respect to the dead, dispatched letters against them to the people stating that it was they whom the generals had ordered to pick up the dead. But this very thing turned out to be the principal cause of their undoing.
[Diod. 13.101.3] For although they could have had the help of Theramenes and his associates in the trial, men who both were able orators and had many friends and, most important of all, had been participants in the events relative to the battle, they had them, on the contrary, as adversaries and bitter accusers.
[Diod. 13.101.4] For when the letters were read before the people, the multitude was at once angered at Theramenes and his associates, but after these had presented their defence, it turned out that their anger was directed again on the generals.
[Diod. 13.101.5] Consequently the people served notice on them of their trial and ordered them to turn over the command of the armaments to Conon, whom they freed of the responsibility, while they decreed that the others should report to Athens with all speed. Of the generals Aristogenes and Protomachus, fearing the wrath of the populace, sought safety in flight, but Thrasyllus and Calliades and, besides, Lysias and Pericles and Aristocrates sailed home to Athens with most of their ships, hoping that they would have their crews, which were numerous, to aid them in the trial.
[Diod. 13.101.6] When the populace gathered in the assembly, they gave attention to the accusation and to those who spoke to gratify them, but any who entered a defence they unitedly greeted with clamour and would not allow to speak. And not the least damaging to the generals were the relatives of the dead, who appeared in the assembly in mourning garments and begged the people to punish those who had allowed men who had gladly died on behalf of their country to go unburied.
[Diod. 13.101.7] And in the end the friends of these relatives and the partisans of Theramenes, being many, prevailed and the outcome was that the generals were condemned to death and their property confiscated.
[Diod. 13.102.1] After this action had been taken and while the generals were about to be led off by the public executioners to death, Diomedon, one of the generals, took the floor before the people, a man who was both vigorous in the conduct of war and thought by all to excel both in justice and in the other virtues. And when all became still, he said:
[Diod. 13.102.2] "Men of Athens, may the action which has been taken regarding us turn out well for the state; but as for the vows which we made for the victory, inasmuch as Fortune has prevented our paying them, since it is well that you give thought to them, do you pay them to Zeus the Saviour and Apollo and the Holy Goddesses; for it was to these gods that we made vows before we overcame the enemy."
[Diod. 13.102.3] Now after Diomedon had made this request he was led off to the appointed execution together with the other generals, though among the better citizens he had aroused great compassion and tears; for that the man who was about to meet an unjust death should make no mention whatsoever of his own fate but on behalf of the state which was wronging him should request it to pay his vows to the gods appeared to be an act of a man who was god-fearing and magnanimous and undeserving of the fate that was to befall him.
[Diod. 13.102.4] These men, then, were put to death by the eleven magistrates who are designated by the laws, although far from having committed any crime against the state, they had won the greatest naval battle that had ever taken place of Greeks against Greeks and fought in splendid fashion in other battles and by reason of their individual deeds of valour had set up trophies of victories over their enemies.
[Diod. 13.102.5] To such an extent were the people beside themselves at that time, and provoked unjustly as they were by their political leaders, they vented their rage upon men who were deserving, not of punishment, but of many praises and crowns.
[Diod. 13.103.1] Soon, however, both those who had urged this action and those whom they had persuaded repented, as if the deity had become wroth with them; for those who had been deceived got the wages of their error when not long afterwards they fell before the power of not one despot only but of thirty;
[Diod. 13.103.2] and the deceiver, who had also proposed the measure, Callixenus, when once the populace had repented, was brought to trial on the charge of having deceived the people, and without being allowed to speak in his defence he was put in chains and thrown into the public prison; and secretly burrowing his way out of the prison with certain others he managed to make his way to the enemy at Deceleia, to the end that by escaping death he might have the finger of scorn pointed at his turpitude not only in Athens but also wherever else there were Greeks throughout his entire life.
Xenophon paints more or less the same picture, but is quite more critical of Theramenes and Thrasybulus, and notes that the proceedings were rushed and the generals were not granted a full hearing:
[Xen. Hell. 1.7.5] After this the several generals spoke in their own defence (though briefly, for they were not granted the hearing prescribed by the law) and stated what they had done, saying that they themselves undertook to sail against the enemy and that they assigned the duty of recovering the shipwrecked to certain of the captains who were competent men and had been generals in the past,—Theramenes, Thrasybulus, and others of that sort;
[Xen. Hell. 1.7.6] and if they had to blame any, they could blame no one else in the matter of the recovery except these men, to whom the duty was assigned. “And we shall not,” they added, “just because they accuse us, falsely say that they were to blame, but rather that it was the violence of the storm which prevented the recovery.”
Whatever happened, and whoever is to blame, all accounts seem to suggest that the trial was highly irregular, a product of the politically charged environment of the later half of the war. Trials of Athenian generals after significant defeats were not uncommon, and a notable example during the war is Thucydides exile, after he failed to reach Amphipolis in time. That said, during the war most Athenian generals that were involved in significant defeats died in battle (or were executed by their enemies shortly after), and thus it's not easy to assume a general reaction of the Athenians towards defeated generals. Interestingly Conon, who had failed in facing the Spartan fleet in Lesbos and later presided over the defeat at the Battle of Aegospotami, never faced charges.
The aftermath of the Battle of Arginusae is the only example of a trial of generals after a significant victory and along with the trial of Socrates are the two prime examples of questionable decisions by the Athenian judiciary.