Silver considers Romney's dismal favorables a "fairly minor factor":

My guess, for what it’s worth, is that we will see some improvement in Mr. Romney’s favorability numbers over the next month or two. It has not been uncommon in the past for a candidate’s numbers to decline while he is actively engaged in a primary, but for him to go through a honeymoon period once he begins to wrap up the nomination.

Harry Enten points out that "every election cycle breaks rules" and lists ones that could be broken in 2012.