Yes there is an easy way.

Go to control assignments menu and find "axis commands" and kick the left and right toebrakes to assign them axis and then create a new default assigments filename and save it using the CFS menu. Lets say its called Toebrakes.

Go to the folder where CFS3.xca is located (not in CFS3 directory it is in (win98) Windows\Application Data\Microsoft\Combat Flight Simulator\cfs3.xca.
In winXP its in (I think) C:\Applications Data\...
Its a hidden file, so tell Windows Explorer to show hidden files and folders.

You will find a brand new wordpad file there called Toebrakes.xca (or whatever name you saved the assignments as from the CFS3 menu).

Find these lines: Action="AXIS_LEFT_BRAKE_SET" Scale="64" Nullzone="36"/>...
                 Action="AXIS_RIGHT_BRAKE_SET" Scale="64" Nullzone="36"/>
---------------

Change 64 to -64 and the toebrakes are reversed!

Be sure to next make toebrakes.xca properties READ ONLY or CFS3 will soon reset the lines above to idefault +64 and you won't have brakes again!.

Peter Dowson (spelling) of FSUIPC fame, was I believe first to find this trick. He also recomends a Nullzone of 0 instead of 36 for full range of brake control on CH pedals (from the controler readmes for FS2002 on his website).  Peter's solution was for FS2002 (editing FS2002.cfg file). But his same trick also works for me when I edited the CFS3's xxx.xca files  as described above. I had same problem as you, now I don't anymore, thanks to Peter!