If you're just getting into photography start with the Nikon D90. I started with a D60 and hated how I couldn't use AF lenses with auto focus because it lacked the in-body AF motor. I upgraded to the D300 within 6 months of owning the D60 (a big mistake, cause I could have just gotten the D90). The D90, though, will drive both AF and AF-S lenses. If I were you, go for it. Don't waste your time with the D40/D60 because you know you'll want to use AF lenses someday!
Don't get me wrong though...the D40/D60 are nice pocket-DSLRs! If you plan on staying with AF-S lenses, then reconsider. The money you save by going with a D40/D60 can be used on much better lenses (17-55mm f/2.8!!!)