It's worth putting the political problems raised by Barack Obama's (relatively modest) associations with William Ayers in a larger perspective.
What few people have recognized is that the political problem he faces is driven by the same underlying problem as the Jeremiah Wright controversy -- namely, the profound mismatch between the electoral context of his Illinois state senate district and the country as a whole.
Here's what I wrote back in March about Wright:
Obama's membership in Wright's church helped demonstrate his cultural authenticity to skeptical constituents in Chicago's black community. But it's created a major problem for him now.
The fundamental problem is that the issue positions and cultural affiliations that won elections in Obama's state legislative district are a relatively poor fit to the presidential election landscape. (They're arguably a poor fit to the Illinois electoral landscape as well, but the collapse of Obama's primary and general election rivals in 2004 let him skate into the Senate without coming under serious criticism.) The fact that he has done so well in the presidential race despite the mismatch is a testament to what a remarkably gifted politician he is.
The Ayers problem in similar. In Chicago, Ayers is something of an establishment figure in liberal circles. Obama therefore had no reason to criticize the former Weatherman when he was trying to build his biracial coalition of white progressive reformers and black supporters. (Of course, that doesn't mean that Obama is somehow associated with or responsible for Ayers's loathsome past, as McCain/Palin and their conservative supporters have charged.)
You can also put Obama's associations with Tony Rezko in a similar framework. It was apparently crucial for Obama's career to have support from wealthy developers like Rezko, but that association now hurts his reputation as a reformer with a clean ethical record.
For more on the idea of district congruity, see the research (PDF) of my friend and co-author Michael Tofias, who finds that "members of the House are more likely to run for the Senate when their districts have high congruity to their prospective statewide constituency."