You guys are making a meal of this :) First off you need to set the throttle and brake axis as combined in order for FS to read the 2 pedals as one axis ie. the rudder. Secondly, you don't need the Logitech profiler software installed to do this as it can be done from the "Game Controllers" section inside windows "control panel" It's only a matter of ticking or unticking a radio button.
I've been using the G25 pedals for ages with a CH Pro yoke so I know it works just fine. The reason I found this thread is because I was searching google for a way of locking the assignments so that when I plug the wheel in each time, FS2004 won't go mad and re-assign everything incorrectly, including the wheel which I want to exclude as I already have a yoke! I know it can be done, just need a reminder as to how. :)
Anyhow, hope this helps a little biteven if it's a bit late. :P