It seems to me that recent history portrays the Christian crusaders as evil and brutal for taking back Spain from the Islamic Moors who conquered them and toppled the Spanish government and ruled over Spain for decades. Why are the crusader considered the bad guys here?
Maybe you are confusing situations:
Currently, the idea of "Reconquista" is just held to talk about the chronological and geographical frame, but the idea of a "managed" process to take all of the Iberian Peninsula back from the Muslim rulers is generally discredited as a "post-facto" fabrication (giving a "national idea" of "proto-Spain" to the several Christian kingdoms, and giving a political justification for their political union).
After the initial Muslim conquest, the Muslim kingdom in Spain became an Umayyad reduct (the rest of the Caliphate came under Abbasid rule) and quickly developed into small Taifas kingdom. During the period, Christian kingdoms fought Muslim kingdoms, true, but almost as frequently the fighting was between Christian kingdoms themselves or Muslim kingdoms themselves. To put an example, the prototypical hero of the Reconquista, the Cid, was employed by the Muslim ruler of Valencia.
The few occasions in which this was not true was in a few cases in which new Muslim groups came from North Africa(Almoravids, Almohads), unified the Muslim kingdoms and charged North. In those cases the Christian kingdoms were (mostly) able to ally against the pressing threat and, in occasion, get support from the Pope who declared a proper Crusade to entice European warriors against the fresh invasions.
As per the Reconquista itself it was, in fact, quite brutal from both sides. Civilian populations were raided from one and other side, defeated soldiers and civilians could be sold as slaves, etc. In some occasions, religious striffe between Muslims and Christians happened even inside the same population at time of peace1 (with Jews being targetted now and then). That said, it was not more brutal than life and war in other parts of Europe or the Mediterranean at that era.
Now, to the point of your question, maybe you are refering to some details of the decisive battle of the Navas de Tolosa, there was a foreign force (called by the Pope as part of a formal crusade). That crusader force defected before the battle; while some authors blame the heat, many others point that the Crusaders wanted to massacre the surrendered populations (of the towns in the way to the Navas), to which the Christian Kings opposed. Of course, the Crusaders were just in a razzia in which all that what counted was the booty they could get, while the Kings wanted to tax conquered towns and not graveyard.
1: For example, the revolt of the Germanies(Brotherhoods)
It depends who is talking.
As @Alex pointed in his comment
Serious historians do not use the words "good", "bad", "evil" etc. These notions depend on time and culture. So when talking about different time and different culture, a scientist should avoid them.
If you take back to 8-9th centuries, you will see that Moors did conquer Iberian Peninsula (being stopped at Poitiers). For Spanish and Portuguese the process of "reconquering" is very important part of their history. They have national heroes of this epoch (eg. El Cid or El Gran Capitán). It's hard to say that (common) Christians (meaning people related to Christian side of the conflict) would say anything bad about the Reconquista.
It is clear that Muslims or Moors (in this case meaning all the people who are more related to this side of conflict), who eventually lost the war, try (or tried) to show their opponent as bad.
Today in (popular part of) history there is a tendency to search war crimes everywhere. This can be the reason to answer your question. What you should remember, this war (or process) lasted almost eight centuries (since Moor invasion until the fall of Granada). For such a long period it's difficult to say who was responsible for the start of war, who was good or bad.
Also, many people find now religious freedom as something very important. It's easy to expect 21st century culture values in historical times, but it can't be related. The process of Converso, along with bad reputation of the Inquisition, also the process of conquests in Americas may add to general view of the Reconquista.