I certainly don't think that the New Yorker cover is the biggest deal in the world, but the basic reason I find it problematic is that I look at it and I think, "Yes, well, that's what the Right says about the Obamas pretty much daily." It channels what they say, but they forgot to add the funny. Hamas loves Obama, he hates the flag and America, he's a Muslim, Michelle Obama is a black militant, etc. It isn't funny to me because I read this crap every day all day. This crap isn't just on obscure wingnut blogs, it's everywhere. G. Gordon Liddy is thrilled.
If in 2000 they'd ran a cover which expressed in various ways things like "Al Gore claimed he invented the internet," "Al Gore claims he discovered Love Canal," "Al Gore grew up in a fancy DC hotel," "Al Gore is such pandering politician that he's wearing 3 button suits and EARTH TONES" (no I've never understood this one either), it wouldn't have been a parody, it would have been channeling the media zeitgeist. The Obama thing? Not so different.
Here's the thing, it is an absolute embarrassment that people believe these things, and I know from personal experience that there is a sizable group of people who do. The New Yorker would have been better served if they mocked these people directly. Unfortunately, what is going to happen now is that conservative commentators (like Gordon Liddy) will point to this cover as clear evidence that Obama is un-American.