It's because coaches like Shanahan believe in their own system so much that they just need a guy to do as their told. They prefer a QB to run the "system" than a qb who can improvise.
Thats the double headed sword of the QB position. Take a guy who can make every play on a whim. Or Take a guy who will make the play that's expected, no more or no less.
I as my own arm chair GM will lean towards the athletes any day of the week. But guys like Drew Brees and Tom Brady counter that argument pretty strongly. Neither of which were star athletes in terms of underwear sports.