It seems like more of the people dissatisfied with Craigslist would be directing their ire at the CEO (Jim Buckmaster), and not Craig himself. Of the two I would assume (perhaps incorrectly) that despite the "Craig" in Craiglist, it would be the CEO responsible for the decisions this company is making...

Craig of Craigslist isn't exactly the same as any old employee of any old company. I understand the distinction you're trying to make, but the fact that it's hard in this case is a side-effect of the context they've worked very hard to create. In other words, they're asking for it.

A corporation is a legal device, but is, of course, made up of individuals. To judge a company is to judge individuals working in concert.

From the OED: "company ... 2 A number of individuals assembled or associated together; a body of people combined for some common object."

When did we stop being allowed to judge people by their actions?

A company is just 1:N people trying to accomplish something (usually earn profit). I would usually agree that it's best to treat a company separate from the individuals there. But in the case of Craigslist it may be fair since Craig has full control of the company, and the companies latest actions are clearly done by either his command or with his consent.

Not to mention his name is on the freaking company! Hard to separate the two when that happens. If you have a problem with Craig's List, why not complain about Craig?

The company, regardless of laws that claim individual rights for corporations, is not something that can be judged independently of the people who comprise it. If you judge a company you are by definition judging it's employees, owners, shareholders, etc. If you are not considering the people, then a company itself is almost nothing.