The Wall Street Journal seems to think it might be signs of something bigger down the road:

American and JetBlue: Partners for the Future? - The Middle Seat Terminal - WSJ

American and JetBlue: Partners for the Future?

Airlines have been a bit like Gangs of New York lately, with several pushing hard to be the big dog in the nation’s biggest city.
Continental Airlines has tried to be biggest in New York through its Newark Liberty International Airport operation. Delta Air Lines is trying to build up two hubs, at La Guardia and Kennedy airports, trying to land more La Guardia slots and expanding its shuttle operation to New York-Chicago, for example, even though American and United already offer scads of flights in that busy market. Despite poor terminals at JFK, Delta has been expanding internationally, too.
American has a renovated terminal at JFK and, it is anticipated, a stronger relationship with British Airways if it can get antitrust immunity. And Wednesday, American announced lots of marketing initiatives in New York, including an interline agreement with jetBlue Airways, which is based at JFK.
The American-jetBlue link is probably more symbolic than substantive. It’s not a code-share deal–the two airlines won’t be putting their flight numbers on each other’s schedule or offering reciprocal frequent-flier program benefits. They can sell tickets on each other’s flight in the same itinerary, but that’s something most airlines can do anyway. American can sell a United Airlines flight through an interline agreement, but it can’t sell the United seat as its own.
JetBlue, which grew up as a renegade discounter offering better service at a low price, has become more and more like a traditional airline. The interline agreement with American is a first for jetBlue with a big U.S. airline–currently jetBlue has interline agreements with Lufthansa, Aer Lingus and Cape Air. Customers can get boarding passes at one stop and check baggage through to destinations.
It makes sense–jetBlue can carry lots of passengers on its domestic flights who come off or or are headed to American international flights at JFK. Discount airlines have always done this–Southwest Airlines carries lots of international passengers at Los Angeles International Airport, for example, even without interline agreements with international airlines.
And American, which has probably seen some (perhaps much) of its customer base in New York and Boston become jetBlue customers as well, can adopt a “join ‘em” instead of “fight ‘em” posture with jetBlue.
It could lead to more, of course. Code-sharing or someday even an acquisition. Who knows? The one thing that is clear – and is good for passengers – is that airlines are clearly focused on capturing loyalty in New York.