The domain name makes the $s through hosting referrals (although you'd imagine that the wp.com self-hosted referrals have long since blown that outta the water) - no idea how or if that rev is distributed.
Automattic, despite being 'barely for profit' (makes me chuckle that, everytime :) would, by my guess, make the vast amount of it's cash through adwords - they used to not show to FF users as they clicked less but they may have changed that now... regardless, they're managed in such a way that bloggers at wp.com will rarely, if ever see them.
Genius, from back in the day: http://pascal.vanhecke.info/2007/11/21/making-money-with-ads...
However, they have also been aggressively monetizing some of their other offerings like http://akismet.com (go try sign up there for free, also genius), VaultPress (kicked us off a few ad spots that one did!) and, of course, 'upgrades' to wp.com accounts.
And then there's the jetpack trojan horse into self-hosted WP installs:
http://wpmu.org/why-jetpack-reallypacks-a-punch-and-the-futu...
VIP hosting etc. has always been a moneyspinner from day 1.
Anyway, if you want a model of how an open source project can be effectively transformed into a money-making beast, while at the same time retaining (if not enhancing) your humble geek GPL cred, look no further.
You might not necessarily like it, but you can't fail to be impressed.
[not really a disclaimer, more FYI, I'm the CEO of http://incsub.com - we have more than a few WP interests...]