Well, I don't think Lee was asking for self-confidence so much as he was asking his father AS the commander of the ship, whether he shared the general view that it was too bad Apollo would be leading this mission because Starbuck would be so much better; he wasn't asking whether his FATHER who loves him (and I believe that he knows this) would feel like Lee needed a boost of confidence...

So I think what Lee was asking for was a professional opinion and what Adama gave him was a familial one, if that makes sense.