You're right, they did dominate. A rather substantial part of that was because UK had zero running ability.
Louisville had problems with speedy backs last year, Williams is that, and Kemp is a mix of power and speed. Horton has trouble making the edge, the O line didn't help him any.
When the 2 backs left the game it limited UK's offense significantly, because Louisville didn't have to be hesitant, they could handle UK's Line and Horton wasn't fast enough to beat them to the edge. Barker did look bad, your defense knew he had to pass, and he lacked experience on how to deal with it.
The constant 3 and outs wear a defense down, and UK's was whipped by that and Trying to contain Jackson.
Towles came in with little pressure, the Cats had blown a big lead, and he still threw a pick in the red zone.
Having said all of that I still believe tha Cards would've won the game even if Williams and Kemp hadn't gone down. Jackson was too much, he has the ability make positive yardage even on busted plays, and the Cats couldn't stop him.