Ayers founded a group that performed bombings and killed people. Obama certainly wasn't part of that (as he likes to say, he was 8 years old at the time), but the fact that Obama launched his campaign at the home of Ayers raises significant concerns about Obama's judgement and what he's willing to do out of political expediency. Obama's continued connection to Ayers throughout his adult political life (see Stanley Kurtz's excellent coverage of this here, here, and here, and Fausta's Blog's roundup retort to yesterday's dismissive article on the Ayers connection in the New York Times here) raises even more concerns.
Contrast Obama's deliberate connections with Ayers for political reasons with Sarah Palin's husband having membership during parts of the 90s with a political party that seems a bit out of the mainstream to most Americans, but which is mainstream enough in Alaska to have had Walter Joseph Hickel, a member of their party, elected Governor in the late 60s and then again during the early 90s.
A lot of what the AIP stands for is stuff I stand for. Personal liberty. Smaller government. There does seem to be a push by some in the party for a secessionist movement to make Alaska no longer part of the United States. But that doesn't seem to be a central and firm part of their platform. The official position on this seems to be just to let Alaskans have a vote on this since they feel they were robbed of such an opportunity to decide themselves at the time of statehood.
Especially considering that Hickel - again a member of their party that ran under their party - was against secession, puts a pretty big block to the claim that the entirety of the party is pro-secession. And furthermore, other than Todd Palin's brief association with the AIP, there doesn't seem to be any actual evidence that Todd Palin was in favor of secession.
The two events are hardly equivalent.