Yes, run the component cables to the tv if the receiver doesn't have component inputs, unless you are willing to trade slightly lower video quality for the convenience of switching thru the receiver using composite cables.
NetCommand is an attempt to simplify things but is not necessary, or even useful, IMO. The idea is that the tv receives all IR commands, and then routes the non-tv commands to other devices. You still have to program it with remote codes for the other devices, right? It's really no different than similar schemes used by Onkyo (Remote Interactive), JVC (Compu-Link), and Sony (S-Control), although those only work with other devices by the same manufacturer. When the tv gets a dvd command, it routes that command to the other connected devices (and the one that recognizes it, responds to it).
Doesn't that sound like the purpose of a universal remote control? An MX-500 will solve all your problems and be far more flexible than NetCommand.