AMR walks a thin line with eagle...most majors prefer to keep their regionals at arm's length so they can whipsaw them, and to avoid being held hostage by a striking regional pilot group.
While AMR risks a COMAIR style shutdown by owning eagle, they were also able to reap the profits from their regional. The regionals (and SWA) were the only solidly profitable airline segment from 2002-2006...eagle's profits contributed to keeping AA out of bankruptcy.
Also the eagle alpa contract is for some ridiculous length of time... 15 years or so? AMR has them right where they want them...wages locked in, no strike potential this side of the horizon.