I don't know why people keep raising the original question, at least in that form. It is the same for ebooks as it is for everything else - each entity along the line continually tries to make as much money as possible for itself. That's true for authors, for publishers, for distributors / etailers like Amazon, B&N, etc.
If the big publishers could pay authors nothing and charge $1000 a book, that's what they would do.
If Amazon (or Apple, or B&N, or...) could charge each consumer $1000 a book and pay the publishers nothing, that is exactly what they would do.
While doing that, they would be trying to figure out how to sell them for $2000.
It has nothing to do with any "reasons" related to cost of printing or distribution or warehouses or marketing or "fair prices" or anything else. Their job, their responsibility, is to make as much money as they possibly can. Everything else is only a rationalization to justify the price.
Ebooks cost as much as they do because either: the sellers think they cannot sell them for more, or one or more entities may offer lower prices for a while than the competition, as one way to try to establish a monopoly, a situation in which they can eventually make even more money than they would otherwise.
Prices are raised at any perceived opportunity, and dropped only slowly, with great reluctance.
The only people concerned about fair prices, or reasons for prices, or anything besides making as much money as possible are the consumers. Everyone else understands what they are about. It is the job of the consumer to act as the others - keep as much of the money as possible. To the extent that ebook prices are higher than "they should be", it is because enough buyers are willing to pay "too much" - we are not doing our job.
If the concensus of ebook buyers, as measured by their purchases, was that 99% by volume of ebooks were worth no more than $4.99, then soon that's what the vast majority of ebooks would be priced at. Book publishers and booksellers are not in the business of not selling books; they try to continue to sell in any market, better than their competition - and continue to do so until bankruptcy. If Congress passed a law that all ebooks were to be sold at $4.99, nobody would exit the business. They would adapt (and also try to get the law changed by paying money to congresspeople).
So the answer is always the same: if prices are too high, it is the fault of the purchaser for buying at that price.