Considering Bitstamp's fees, $5M shouldn't be a problem for them. They are a huge exchange and they make a lot of money.
The Bitcoin exchange business has low commissions, and they're heavily discounted for big traders. Sometimes all the way to zero. It's hard for an exchange to raise prices. So exchanges tend to look for other ways to make money. Those ways usually aren't good for customers. Trading on one's own exchange and front-running are tempting. Mt. Gox probably did that; many users observed that, during busy periods, trades did not appear to be first in, first out.
That's why no major financial firm has entered the Bitcoin exchange business. It's not very profitable.
And the amount of bitcoin transactions has only grown since 2013. e.g. the record highest number happened just yesterday. Or compare wallets at the top bitcoin company right now which verifies users and bank accounts, Coinbase, which was at 700k wallets this time last year, now at roughly 2 million. Another 300 million of VC money was invested since 2013 into the bitcoin space.
I mostly agree on your larger point regardless, big traders get discounted (any source for that from any particular bitcoin exchange, btw?) and exchanges are definitely not gold mines right now. Look at Vault of Satoshi, just closed. It ran well but it just wasn't bringing in the type of revenue they could with the amount of expertise they had on board. They've switched focus to a Netflix app. But comparing 2012 Mt. Gox to 2014 says quite little, we're talking about a trainwreck of a company here in an industry that's seen 1, almost 2 orders of magnitude growth since 2012. If price is a good proxy (not really great, but sorta ok), the fiscal year in which Mt. Gox made the $1.3m revenue / $300k profit started with a bitcoin price of less than $5, for perspective. Things have grown somewhat since then.
Their volume and bitcoin prices were crazy high a year ago, I estimate they made around $6-10M.
Huh, what?