I imagine hardware and software compatibility plays a fair part in keeping them separate, the X360 and PS3 are fairly different to PC's and each other in a lot of ways. Keeping the consoles separate from each other would be easy, its not like you can put in an IP Address manually when you want to find a server. PC's to console servers, probably by use of a firewall or proxy, since you aren't connecting through PSN/Live matchmaking its rejected, coupled with plain incompatibility.
Using a PC to play on console networks, I imagine to do so you would need to emulate the consoles, which is basically mimicking its hardware and OS, and hope that it works. Though I think if you tried this you would set off whatever anti-cheat protections are on the server.