The yearly fee is NOT to pay for any costs; the fee is a tactic to keep low-effort spammy app developers out, and therefore to reduce the load on the review team. The $99 fee does not cover the costs and expenses that Apple does and has done for you as an app developer. Dropping it would not affect their revenue directly, but it would open up the floodgates of random app submissions.

One could argue that the Mac hardware itself that you need to develop iOS apps is a similar barrier to entry though.