Right know, Milkshape 3D is the best to use for FL because it's the only one able to export to CMP format. (There's a trial version available)
But you can try some other free programs such as GMax (a free, mod oriented version of 3DSMax from Discreet), Wing3D, Blender, etc... or trial versions of Rhino3D, Lightwave, Maya and some others...
That's probably the best way to make your choice.
The problem with all these tools is that they're not all adapted to low-poly modeling and you won't be able to export your work directly to FL. As far as I know, you're obliged to use Milkshape for that...
Personnally, I use Milkshape and I'm very happy with it. It's cheap, powerful, it's quite easy to learn, it can be used for a lot of games and it's certainly the best for texturing...
--------------------------------