Ok - fine, maybe 5% of web applications require the features of J2EE. Go ahead and build your site with that.
If you don't need those features, why not buy 10 commodity linux boxes (a la Google), build your web app in PHP and throw a monster load balancer in front of them?
I think it was Joel Spolsky who was describing the main two kinds of programmers he comes across:
1) The kind who love really obscure, theoretical CS problems. They'll spend a week working on some super neat-o solution to a binary crypto algorithm <or whatever>. These kinds of people love Java. It gets them all hot for some reason.
2) The kind who are interested in solving real problems, and doing it quickly and efficiently. They'd rather write 5 lines of PH code to get a job done, instead of 25 lines of Java to do the same thing. Who cares if it doesn't look as good on the resume?
There's this obsession with Java in big IT departments now as if it's some kind of holy grail. All of the "breakthrough" sites like Yahoo, eBay, etc. were built in 2 weeks in some kids garage. Trust me, the next ones are going to be built the same way & it's not going to be with Java/J2EE sitting on $100k hardware.