I'm not Obama nut. In fact, I've been one of his more vocal critics on this forum. But I have to disagree on some of these points:
First, regarding the flag pin. You're right to point out that saying "wearing a flag doesn't make you a patriot" isn't really an on-point answer to criticisms of Obama refusing to wear it. But I don't think that refusal implies anything negative about Obama, either, other than, perhaps, that he suffers from an unfortunate lack of political pragmatism (since he's opening himself to cheap shots for no good reason).
On some level, I respect someone who has decided not to cheapen his patriotism with shallow displays. It's akin to the biblical injunction not to give alms in public and not to pray on the street corners. Just as charity and faith are more genuine when they're not being done to win public praise, so is patriotism. But, as I said, pragmatism dictates that a politician should pick his battles carefully, and this one wasn't worth fighting, for Obama. I'd say the same regarding placing your hand over your heart for the anthem (though, in that case, Obama presumably wasn't making a pointed gesture, but rather simply forgot himself).
Regarding the Reverend Wright, I think it's relevant, but not necessarily highly important. The choice of Wright as a spiritual advisor could imply several things, and it's hard to say for sure which is the truth:
1) Obama has horrible judgment in his choice of key advisors -- that Obama completely misread someone even after years of very close association. Obviously, that's a big knock on him, since as president one of his very most important skills will be the ability to select good advisors for key adminsitration positions. If he lacks that skill, he probably will be a bad president, much like Bush (who surrounded himself with horrible human beings like Rove, Cheney, Rumsfeld, Wolfowitz, Feith, Rice, Ashcroft, Gonzales, etc.)
2) Obama judged Wright correctly, and was in agreement with his radicalism. Obviously, that's going to be an issue for a lot of Americans, given what came out of Wright's mouth.
3) Obama was just using Wright as an "in" with his district, and didn't really pay much attention to Wright because he regarded him as nothing but a political prop. Poor taste in political props isn't a very big knock on a president, since someone can have great wisdom and judgment on things that matter, while being a little careless on lesser issues. However, some people would then find Obama's sanctimonious displays of religious faith to be a sign of poor character, if he hadn't been genuine about the importance he purported to ascribe to the church and Wright in his own spiritual and moral system. He comes across as a calculating jerk who only pretended to care about Wright and the church, but that may or may not be a big negative for being a good president (I don't think it's a big knock on him, since I think most politicians only pretend to care about their religious advisors and churches, to make themselves more popular with the voters).
4) Obama compartmentalizes religion from other aspects of his life, such that he is capable of hearing things said by a religious leader that he strongly disagrees with, without it really registering as relevent to his real life. This would be the possible explanation that would put Obama most in line with other people. I know lots and lots of religious people who claim, in an abstract way, to be adherents to a faith, while they firewall that faith off from the rest of their lives. For example, I know a lot of people who claim Catholicism, complete with a claimed belief in papal infallibility, and yet they believe in allowing divorce, or the death penalty, or they object to the church's stance on homosexuality and gender roles and birth control and in vitro fertilization, etc. These folks can sit in a pew and hear a priest say the most ridiculous stuff, without objecting and without seeing it as a reason to leave the church, because it's a compartmentalized area of their lives that operates by different rules. If Obama has a similar mindset, that's a bit of a knock on his intellectual honesty, but not much reason to question his likely performance as president, since most presidents have had similar mindsets. Heck, Nixon was a Quaker, right? I'm sure he sat quietly through more than a few sermons advocating radical pacifism, without that having much impact on his conduct as president. Similarly, the mere fact Obama probably sat quietly through sermons full of Wright's radicalism isn't necessarily a reason to think such sentiments would be reflected in Obama's choices as president. He can be called a hypocrite, of course, but how many presidents weren't hypocrites when it came to religion?
Now, about Michelle Obama's comments on having never before been proud of her country. Personally, I was a bit irked by how little media exposure that got, because I know that if it had been Bill Clinton saying something like that, Hillary never would have heard the end of it. The Obamas get to play by different rules than the Clintons, as far as the media is concerned. But, in the end, her comments shouldn't be a huge deal. It's the kind of loose rhetoric you expect from a non-politician. Even if we take her at her word, so what? She's not running for president, and Obama's choice of her as a wife just doesn't reflect meaningfully on his likely conduct as president. So what if his wife is a bit of a self-involved twit in regard to her attitude towards her country?! Big deal. I'm sure, from Barack's perspective, that's got to be pretty far down the list of what he was looking for in a "significant other." A lot of us are married to people who don't share our beliefs in one area or another. But if they're kind and loving people, who share our beliefs in matters that are central to marriage, like child-rearing and fidelity, and if we enjoy spending time with them, and share interests and beliefs in other areas, we overlook that disagreement. Why hold Barack's blind spot against him?
Now, on to Ayres. If Obama says something to imply he approved of Ayres's methods, that's going to be a big problem. So far he hasn't. The fact Obama has spent most of his adult life working peacefully within the system to bring about change strongly implies that he thinks Ayres's methods were counter-productive. I don't think that's countered by the mere fact Obama has a relationship with Ayres 40 years after his objectionable activities. It's just not justification for thinking Obama somehow approves of what he did.