First, the whole 'local boy' talk is utter nonsense. Winning puts fans in the seats - not some guy from the local neighborhood. If Alex Smith is better, they'll forget where he's from in a heartbeat.
Second, the "Rodgers is ahead of Smith" is not referring to the overall rating they have, just with reference to his background of operating in a more pro-style attack. That says nothing about the "upside" of both - and I think it's clear that Smith is viewed by both SF and Miami as having more upside.
Third, as others have noted, SF is doing this to be smart. They control the draft and they are not going to just give up control just to sign a guy. It would not be good for the franchise. If they signed Rodgers and then watched a bidding war for the #2 pick result in multiple selections for us - they would be fools. I think they are playing it smart.
Finally, they probably do have Smith as the top player on their board and if they don't get a significant offer to trade down, they'll take him - Unless, they feel he will be a major holdout. It all comes down to weighing out those options and the relative ranking of Smith & Rodgers. Of course, they could throw everyone off and go Braylon.