I use my middle name pretty much everywhere. At work I used to book travel myself and would always book under my first and last name. We recently hired an admin who booked travel using my middle and last name.
Jet blue refused to change the ticket (or perhaps wasn't able to?). The only option was to cancel the flight and re-book it at the last minute price, of course. The other option is to show up to the flight and risk TSA refusing to let me travel.