I 'am really curious as to why Microsoft has not connected these two servers? I see absolutely no reason to why Xbox Live and Windows Live should not be connected and be able to both participate in the same online matches and other online games. I mean if Final Fantasy 11 can connect Xbox, PC and PS2 altogether on the same servers why the hell not for things like Modern Warfare 2 or Bad Company it truly doesn't make a whole lot of sense. 

XBL Gold subscription fees. If people are playing on 360, more money for MS. If their friends have to get a 360 version and their own XBL subscription, even better.

On top of what Bigandtasty brought up, developers tend to have a hell of a time balancing the two as console players will whine that PC players will be more accurate with a mouse and vice versa. There have been games that mixed the two (Shadowrun comes to mind, which was rather successful at stifling the whiners) but said games have required Live gold subscriptions regardless of what platform you where playing on.

They've done it before, but like @Driadon  said, there aren't a whole lot of games this could really work with balance-wise.

why the hell not for things like Modern Warfare 2 or Bad Company it truly doesn't make a whole lot of sense.

Well neither hold an advantage if you ask me. When I played Shadowrun, no one seemed to be that much quicker to the aim that I couldn't handle on a controller. A very skilled console player can match any PC player, easy. The only time I could see that failing miserably, is if they let PC gamers play Red Alert with xbox folks. THAT's when the speed of the mouse n' keyboard come in handy.