Both American and JetBlue had submitted bids for the service; at the initial filing Jetblue's package was several million dollars more. However, they were allowed to resubmit a proposal on June 2nd which turned out to be much less and comparable to AA's (revision). By my initial search it doesn't appear that any media outlets reported this change.
The impression of favoritism set aside, it's disappointing that AA's bid wasn't taken more seriously given it would have increased flight frequencies to 12 a week from what will stay at 7. While there has been a lot of passion in the local community for JetBlue, a more rational analysis would have been preferred.