All Atlas V first-stage engines (RD-180) are manufactured in Russia. That the second stage engines are made in the US doesn't change the fact that you're dependent on Russian supply.
In response to your edits:
>but they can't get more flights because of their record
The Air Force required 3 successful flights in the exact configuration the Air Force would fly. SpaceX provided the "record" as stipulated by the Air Force, which nevertheless committed to a large block-buy contract with ULA. By the Air Force's own standards, the billion-dollar subsidy is not necessary for their needs-to-get-to-space payloads.
Also, "the other companies" is just a single supplier, ULA.