As of now, naked domains ( example.com ) are not supported by App Engine.
Instead you can make a Web Forward from example.com to www.example.com. This can be achieved in various ways depending on where you've registered your domain and if the registrar offers DNS services.
If not, you can use Zoneedit:
- Sign up for a free account at zoneedit.com
- Create a zone for your website
- At your domain registrar, change the name servers to nsXX.zoneedit.com (multiple nameservers - these addresses can be found the page of your zone)

- Create an alias for your www subdomain that maps to ghs.google.com
- To make your site accessible from the naked domain, add a webforwad from domain.com to www.domain.com

- Zbang! You've got a working website, that is accessible from both the naked and the www subdomain.
These changes might take some time to propagate
On the google apps page you had to add thee www web-address on the applications settings tab
(what in my understanding you already did)
Hope this helps, and if not you, then maybe others :). + zoneedit is a great & free tool for DNS management, and you can also define custom mail forwards and stuff :)
(Ps. the screen shots are taken from a working app engine example site that runs from www.secondhand-extra.ro )