Yes. Type into google.com "D5000 review" and then "D5000 problems". Do same for the other one.
Most every honest review you read tells you how much cheaper D5000 build is compared to D90. It's both flimsier and includes less rubber grips. It wasn't made for professional, instead it was made for an entry level amateur. Think in terms of camera's longevity!
Now, I'm not a pro at all. But if I'm going to buy into this new DSLR photography fad, I want something that will last me, hopefully, a life time. If I'm going to spend a $1000 on a camera, I want it to last! This means I'm getting what pros have, D90 minimum for Nikon. Know why? Because fads don't last long. Build quality of D5000 shows it.
Finally, go touch them in a shop. Touch D90 and D5000. The difference is obvious!. You don't even have to touch it, you can see difference in build quality from a few feet away, as you looking at them in display case. D90 looks like a different camera. Sure D5000 has a flip out display; here is my advice compare its flip out display to one from an Olympus.