I believe the OP is referring to NFL fans' perception of Harbaugh, not 49ers' fans.
Harbaugh is a punk, but that is not illegal, nor a problem for a franchise. Unless the guy is breaking the law, it doesn't matter how many points he scores on the likability scale. In the NFL, it is all about winning. Now, if players begin to turn on him, then that is another issue. But, there is no indication that is the case. Winning solves everything. If he starts to lose, then fans will turn against him. Bill Walsh was considered a punk by many as well, but the guy simply won.
As for Harbaugh scrambling to create a revisionist history of what happened with Manning and Smith, it is ridiculous. Everyone knows he actively pursued Peyton. And, why not? If you have one of the all-time greats sitting there on the open market, you have to make a run after him. As much as I like Alex Smith the person and competitor, to not actively pursue Mannng would be silly. Harbaugh should have simply not addressed the issue with the media.
In the end, would we like to win, and also have a classy, likable coach? Sure. But I think 49ers fans would gladly have a guy on their sidelines that is not well liked, but wins games.
[ Edited by MadDog49er on Jun 11, 2012 at 7:57 AM ]