I thought he sounded more bored and reluctant than anything. Like he didn't really believe it, but he had to do it because the script told him to.
It's called self-doubt because he can't fully deny it. Raynor knew by the time of the Brood War, Kerrigan already commanded enough Broods, but the UED had the Psi Disruptor which could interfere with her control.
Combined with the way the UED defeated the Dominion, it's obvious they're a forced to be reckoned with. Do you really think Raynor would have just ignored them completely?