Hey guys. :)
To address the original question, we plan to offer paid add-ons, but we're not going to charge for anything you get for free now. We've been testing out some things like domain parking and custom themes, and as our billing system gets ironed out we'll start to make more of these upgrades available.
We have taken a small amount of investment, as I blogged about here, but we haven't really dipped into it here yet. Everything WP.com currently runs on has been bootstrapped by personal money, Akismet licensing, and (as drmike pointed out) hosting partnerships. We're planning an expansion to make things faster and more reliable, that's what we'll be using the investment for.
I can confirm that we're not a CIA front, at least as far as I know. What's a little spooky though is my father did work at Brown & Root (which merged with Kellogg, which became part of Halliburton) for 25+ years, but I believe he consults for Chevron now. (There's not a whole lot in Houston besides oil and medical!)