He certainly could veto it. But Obama signed both the Small Aircraft Revitalization Act of 2013 and the first Pilot's Bill of Rights Act back in 2012. That's a good sign that he'll approve this one.
One factor in favor of his approval of the new bill is that the second Pilot's Bill of Rights act is bi-partisan. Vetoing it, he'd tick off members of his own party. With the Democrats the minority party in both houses, he really can't afford to do that.
Of course, there are some aspects in the bill NOT related to pilot medicals that may generate their own controversy, and certainly a non-related "poison pill" rider could be added that would guarantee a veto.
Ron Wanttaja