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Update: Shortly after I contacted Amazon customer service, my account was upgraded to prime. I haven't checked with friends to see if they can use their emails yet.

The problem might be that subdomains are often assigned to people/groups affiliated with the university who can then run their own mail servers under that subdomain. This makes it trivial to give an email address ending in .edu to people who aren't students.

Since in my experience Amazon's customer support people are actually people, they might be able to make an exception for your particular domain if you contact them.

I don't think I ever had a me@domain.edu address in school. There was always an vestigial environment name in the middle (@eos.ncsu.edu and @titan.sfasu.edu)

I go to Notre Dame and we have Google Apps. Our emails however look normal with a @nd.edu domain and the sign up worked for me.

my guess is it's because you have two periods in the @... section

nope, works with my mail.utexas.edu email.