I have flown a connector through to Orlando via Jet Blue. All but one trip with them was fantastic. This upcoming trip with my sister it was cheaper for me going down to do the connector through JFK, but coming home it was cheaper to do the Nonstop.
The only time we ever had a problem with Jet blue was last year when they basically fell apart with the Valentines day snow storm. We got stuck in Orlando and ended up flying home another carrier. They were great with thier customer service after with us and made up for the 28 hour delay.