I thought Peyton's injury was, in large part, a genetic issue - which is what kept his older brother, Cooper (who has often been said to be the best football player in the Manning family), from having a long football career. I wouldn't be shocked at all if multiple hits he took throughout his career exacerbated the problem, though.
In 2011, Dungy came out and said he thought that hit in 2006 was the root of it, though. He said it was right after that when they started cutting his throws back in practice, etc... it was a pretty nasty hit (http://www.nfl.com/videos/indianapolis-colts/09000d5d8275f9af/Did-Redskins-cause-Manning-s-neck-injury)
Definitely, my grandfather lived in Baltimore for a while and grew up watching him. He still pulled for Indy but always referred to them as Baltimore. I wasn't allowed to say the name Irsay in my house. The game sure has changed. I wish I could go back in time when players didn't get flagged for breathing on a player and defenses were actually feared by offenses.