This seems like one of those phrases that has become so idiomatic that it may be pointless to deconstruct it. We use it in the context of derision or disapproval:
Patty: Pat Robertson is nuttier than a squirrel turd.
Bystander: Yeah, it takes all kinds!
Clearly, the bystander is in full agreement. But the phrase still throws me. Strongly implied within the phrase is "It takes all kinds [of people] to [achieve some result].
Most of the Google hits seem to imply something positive about the phrase, like biodiversity (“It takes all kinds of people to make a world”).
I always took it to be a phrase you use when someone is very different from you, as a way of shrugging off the difference. Like, “I would never (insert odd behavior), but I guess it takes all kinds.” I believe the full phrase is “It takes all kinds of people to make up the world,” or something similar.
I don’t think the bystander was completely agreeing. I think he was agreeing that he was nutty, but not malicious, which I’m guessing was the implication in Patty’s statement.