You have to quickly double tap one of the beginning motions of the ultra. Like with Balrog, sometimes I dash ultra through fireballs, so when I do that I input: b, ff, b, f + PPP. So to flashkick -> ultra with Guile, you need to do: db, ub + hk, mk+mp, bb, f, b, f + PPP. Forward dashing out of the focus works as well, but the timing is a little different and he can cross under the opponent, so you're better off back dashing. It's easier said than done though; you have to be pretty fast with the inputs to pull it off.
Dee Jay can also do something similar with his U2. You can do EX machine gun upper, forward dash, ultra. His is way harder to do IMO.