Where's the irony? Matt thinks proprietary software has its place, and he likes free (as in beer) software.
He's not ignoring the great free software, he's pointing out that only using free software means that you give up using proprietary software in the cases where it is better.
I do have one blog on MT and one on Wordpress, and to be honest I'm not sure which I prefer. It's a close call either way. Given what I've heard of Wordpress's scalability issues, I think I'd use MT if I were running a blog with the expectation of large traffic numbers.