The next time you see something you don't understand, your automatic reaction shouldn't be "those greedy bastards", it should be to actually educate yourself as to why it's being done. You may find that in a lot of cases there are actually really good reasons for it. And even if you decide that you don't agree with the reasons, that doesn't make it appropriate to accuse someone of being greedy or doing "evil" things (e.g. artificial technology barriers to extract money), and it's rather offensive for you to do that.
It doesn't matter how much it costs. Even if it only costs $0.01 a year it would offer the same level of protection.
The only thing the fee does is limit the number of developer certificates to one per bank account.
Obviously, the $99/year isn't making Apple a lot of money. But what it is doing is creating a culture of acceptance around Apple-as-gatekeeper. The iOS app store is most certainly making Apple a non-trivial amount of money (yes I know its a small percentage of their total at the moment.)