Your question is well meaning but is a little misleading. Nobody goes to a service academy to "play football, etc." They go to a service academy to get an education and get commissioned as an officer in the armed services. While doing that they may play Div I sports or not, but it is secondary. If a Div I athlete chooses to no longer play, he does not lose his "scholarship" and is on his own dime for college, he continues on along with all his classmates. Having said all that, the service academies have also chosen to play Div I for the money it brings in (like all the other Div I schools) and they do go out and look for gifted athletes and give them a good sales job on the Academy. It is a hard sell (No NFL afterwards, no fun and games during the off season, no beautiful coeds flocking around....) and they offer no rose garden but the toughest college education in the country and a head start on a military career. The young men and women who respond to that challenge are few.
The young man or woman then has to go through the same application procedures that every other candidate does AND they must meet the same standards as everyone else. The Admissions Boards most certainly know of a coaches recruitment efforts and they may or may not take that into account in selecting the appointees. If the candidate is below the academic standards, they may be given a year at the prep school or a foundation prep school before entering. I know, there are a million stories of abuses out there but that is the way the system is set up and that is what I think you asked. As much as a kid may have a great throwing arm, if there is doubt he can hack the Academy academics, he is not taken as the service academies absolutely hate to experience drop-outs or flunk-outs. There are NO easy majors at a service academy.
As far as congressional nominations go, they only fill roughly half the entering class. The remaining nominations are presidential, vice presidential, superintendent, and whole slew more. That is where nominations are awarded from if none is gotten from a member of congress. It is not a perfect system but the final goal is skewed to begin with.