Hi Missile,
First thing first there is no such thing really as a beginners camera, A total newbie can pick up a 1Ds mk3 or 5D mk2 and start shooting straight away. What i would say is try and spend as much as you can on quality glass as this is so much more important than worrying about bodies. Also don't get too caught up on Pixel quantities. You can print up to A4 no problems with a 5 mp camera. Both cameras you mention are fine but buy the best you can afford. Also read up and go onto Youtube as they have some great free snippets on how to use a DLSR properly.
In the first place, why you shortlisted D90 and D5000?
You can review and compare both spec, price wise D90 is perhaps 200-300 more than D5000, so depends on your budget.
As mentioned by others, non AFS lens do not auto-focus on D5000.