The best defense is a good offense
If we only defend, we lose the war ~ Kembai Shimata.
This answer will not duplicate the thorough resources analysis a couple of the others did, but approaches the question based on the strategic concept of the Japanese war effort from 1937 through about 1944 - after which point the noose had began to tighten, US unrestricted submarine warfare was squeezing the Japanesse economically, and the end was a matter of time once (1) the US were back in the Philippines and (2) the Island hopping campaign ground to its inexorable conclusion. The Japanese loss of the carriers at Midway, and the loss of a great many pilots during the Marianas Turkey Shoot, left them without the resources to create a better air defense scheme similar to that adopted by the Luftwaffe from 1942 - 1945. (And they had their own resource problems).
1. The Tokyo raid happened while the Japanese were ascendant - before Midway
Before Midway, and after Pearl Harbor and the overrun of the various European/American possessios in South East Asia, Japanese strategic view remained tied to the "multiple rings of defense" mode: they kept expanding the outer ring of their bases to make it harder and harder for American planes to reach Japan. Expending precious resources on air defense rather than making it harder/nigh impossible for American aircraft to strike Japan was counter to that strategic template.
2. A success on Midway would render future raids moot/too hard
The Midway operation was a logical continuation of the strike on Pearl Harbor: the long game was to convince the Americans (and others) to negotiate a ceasefire/end of hostilities by being in a position that was too much trouble to try and overcome.
On September 4, 1941, the Japanese Cabinet met to consider the war plans prepared by Imperial General Headquarters, and decided:
Our Empire, for the purpose of self-defense and self-preservation, will complete preparations for warGGranted, Yamamoto's reservations about the Empire awakening a sleeping giant eventually came true.
"We can run wild for six months or maybe a year, but after that, I have utterly no confidence."
3. The Doolittle raid was a spoiler raid/psychological operation
It was as much intended for domestic consumption, in the US, as it was to let the Japanese know "we can reach you, and we can hurt you." But if you look at the size of the raid, and compare it to raids launched in 1944 and 1945 from Island bases, it was puny and hardly could be expected to do more than send a message. The Japanese, correctly from their strategic position at that time, didn't use the Tokyo raid (April 1942) as a sign that they needed to make any significant change.
And by the time they needed to make that change, it was (1) a bit too late and (2) a matter of scarce resources as mentioned in both rs29's answer and JMS' answer.