All miles previously accrued using the shared system won't be affected, and you will still earn them on any flights already booked up until April 1st.
This is a total bummer for those that frequently traveled on JetBlue to and from Boston Logan and JFK, the two airports that ran routes eligible for the frequent-flyer agreement. If you are only a member of JetBlue or American's program, be sure to sign up for the other so you can collect miles going forward.
The silver lining amongst this disappointing news is that American and US Air are working out their own frequent-flyer collaborative program. In case you didn't know, you can now earn and redeem miles from both programs on either airline.