Rogan is definitely not alt-right but he has absolutely no problem with giving them air time. He also gives hard left-leaning people like Matt Taibi airtime as well, though.
I don't really think of him as a free thinker though, I just think he's not really smart enough to challenge any of these people intellectually, he just likes the pretense of having "intellectuals" on his show.
Honestly, I enjoy the guy, but he gets way more credit for being smart than he deserves. Smart people have opinions and ask hard questions, they don't just let people say dumb shit unchallenged.