I just rewired my CH Pro Pedals USB so they could plug into the Gameport connector on my HOTAS Cougar. Once in game, I went the ship control options, clicked on the axis control for roll and moved the pedals and viola - the game saw them just fine - same method works for the Cougar throttle as well.
I was disappointed that I could not set the move left and move right commands to the toe brake axis and perhaps the move up and down to the rotary axes but oh well

Pedals work great with roll.
Before I rewired the pedals (much soldering was required along with dremel tools) - the pedals I don't think could be assigned as the game only recognizes one input device.
And no, I didn't go through all that work for FS 2(though I love the game), I play a lot of flight sims - i.e. IL2 FB+AEP/Falcon 4.0/Longbow 2 etc (hence why I have a cougar) - but I hope this helps you answer your question.
In other words - I have ALL my devices routed to my PC through ONE USB plug - through my HOTAS Cougar (I think it has something like 9 or 10 axes in total).