So, apparently, it is ok if someone can pay for such airtime out of his own pocket, but not if twenty people pool their pockets to pay for it.
Is this one of those, "If you can't do everything perfectly then you shouldn't do anything at all?" It's true that McCain-Feingold only dealt with corporations. It's true that it was not the end-all of campaign finance reform. So what? The law still had a big impact, and a positive one if you're someone who cares about the corrupting influence of money. Soft-money spending (outside organizational spending) tripled between the 2008 and 2012 elections.
Your concern about "the rich guy" getting heard where the paupers contributing to Citizens United are ignored is misplaced - they're all rich guys. PACs are for rich people and no one else. Anyone with less than $5,000 to contribute just gives it directly to the candidate's campaign. Further, your implication that corporate political spending is just a bunch of like-minded people pooling their money is ridiculous. If I work for Comcast does that mean that I hate anti-trust law and net neutrality? When Comcast spends the tens of millions of dollars that it spends on politics, is it representing me or is it representing just the few people at the top who control how the company spends its money?
Yes, McCain-Feingold blocked spending by non-profits and unions as well as for-profit companies. Some few of those might have been groups with legitimate political interests as you describe. Doubtless those just told their members to make political contributions directly, thereby ensuring that their members still had their speech intact. And if the organization itself can't speak? Companies don't (shouldn't) have first amendment rights.
Ultimately the best argument against the Citizens United decision is to simply look at its consequences - the vast leap in political spending, with so much of it from completely unaccountable anonymous donors.