I have:
1) signed up for an aws account
2) set up buckets for domain.com and www.domain.com
3) enabled website settings in properties for each domain
3)
Sounds like your DNS/Name Servers on GoDaddy aren't set up right. They should have the information listed for the Nameservers somewhere where you're hosting the site.
EDIT: I've done some more looking around and it would Amazon doesn't provide you the Nameservers for S3. The "real solution" to this would be to set up a CName on GoDaddy. This site provides a lot of insight on doing that: http://www.google.com/support/blogger/bin/answer.py?hl=en&answer=58317
Also, this question seems to have come up before: Using GoDaddy Domain Hosting to link to Amazon S3 Website