First, all major college programs skirt around the rules in some way. I have no doubt that in big college programs, players are paid, always have been and always will be. SEC schools are probably the biggest offenders in this regard IMHO.
Second, maybe Bill has gotten a little more of a bad rap than he deserves, but obviously some folks in college football are leery of him. Once that mindset has set in the people who are in charge, it can take a long time to erase it. Otherwise, I feel he would be mentioned prominently when these searches happen every year. But, you rarely hear his name mentioned, and winning coaches at these type programs need to take advantage of their opportunities when their name is hot. Before long, he won't be hot and his future prospects will vanish like a fart in the wind.
I hold no ill will towards Bill, and he's done a great job at UAB. If UAB is good enough for him and his family then more power to him.