Considering how many mutants that have exsisted for the last few years and Cyclops disregard for basic orders, Cap's under no obligation to believe that the joining of the Phoenix and Hope will result in the flourishing of Homo-superior. That plan could backfire and then eveyones doomed. Finally, remember it was a mutant who started all of this.
Really? REALLY? She was AN AVENGER!!! One Cap refused to negotiate for. REFUSED TO NEGOTIATE!!! And when the Avenger decimated an entire race... did Cap even say sorry? Or care? This is EXACTLY what I mean. He doesn't negotiate, he doesn't give others (who are telling him they "can't contain Wanda much longer") the benefit of better knowledge. He's a class A hypocrite!
"I don't know how to please you Lord, but I think the fact I try to please you, pleases you."