This has been really annoying for me as well - Kayak has always been the most efficient and least bulky way to search for airfare and now Jetblue fares are nowhere to be found.
What I find stranger is that no one is talking about this online - when American started withholding their fares last year, it was a huge public debacle. I received an email from American rationalizing their decision and the story was covered by many news outlets nationwide. Yet, for some reason this has gone by completely unnoticed.
I understand that Jetblue is not AA, but one would think that someone would be making some noise...