It may be free for weekend projects but if you're planning to get some serious traffic, prepare for some hefty bills.
You probably wouldn't want to run Reddit on App Engine, but anything with medium traffic or decent monetization should work out just fine.
The only other caveat is that it may depend on what the app does and how you utilize the datastore. If you don't consider cost of the datastore when building an app, it could end up being expensive like you mentioned.