The CD protection is a pain in the rear. I have to put it in, start up the game, and then take it out to put in a music CD for atmosphere (grin).
The thing is, there are tons of sites that tell you how to bypass the protection or supply utilities, or patches, that accomplish the same thing. Any good developer can simply run the game from a debugger and figure out how to hex edit the .EXE so that the CD is not required. CD protection is not overly difficult to bypass.
I am glad to hear that the CD stops being required after awhile (I assume it works like it did for Flight Commander 2). I can live with playing "CD swap" but I question the point of adding protection that, with the right tools or knowledge, can be bypassed with a little effort anyway....