There is still a little talk around about exchanges closing and hitting the road and, yes, this happens frequently, but not that often as an outright theft. It is simply, when done right, too profitable to walk away from.
Think about an exchange like YoBit, I picked them because they are popular, well-known, and obviously my sig-camp.
There are some expenses and especially in the beginning this is likely where most will fail. There are licenses that you need to get and those are expensive and require other things that can get pricey, like an actual office. We are approved as a MSB and there is an inspection of sorts, basically showing that you are not in your garage. The license itself is pretty cheap. State to state there are fees and such, but in the end it is not that bad.
Then, you need the cash in hand to be able to trade back and forth for some time without liquidating your coinage. That can be about $10,000-100,000 depending on how volatile you are willing to be. But, once all is said and done and you get a good number of people trading, it is a VERY fast paying business.
1. EVERY trade pays you a fee. So, every time someone sees a new coin and buys it, then shits themselves and dumps it back to BTC or whatever, there is a fee.
2. Most new coin owners pay to be on your exchange or pay for an ICO
3. Many people deposit BTC and other coins in and never hit the point where there is enough to cash out. A minimum withdrawal amount combined with a withdrawal fee, YoBit charges 0.0005 to withdraw BTC, means that most newbies that find BTC and play around only get enough in their account to get disappointed and never withdraw the coins. This is not technically the property of the exchange, but(like banks) they can leverage that unused coin amount, combined with others, to do more business. Also, I am sure that buried in the T&C, there is an amount of time that can pass and the coins are theirs to keep.
4. Fun things take money too. I can never say enough how much I love the "Dice" link on YoBit. People trade and trade and play faucets and rotators and all that and then one of two things happens to a lot of folks. There find that there are withdrawing a very small real amount, like two bucks in the real world or they are below the minimum withdrawal, or they are feeling great about just making five dollars trading and................they hit the dice link. That is just slightly less than a fifty/fifty shot, meaning you will likely loss.
After you have made you small fortune, after you have slaved at the faucets for six weeks or whatever has gotten you your measly little ten dollars, you still have that one more chance to hand it all back to the exchange in the dice game.
I believe that most exchanges, barring Cryptsy, that bail and run are simply at the end point of months or weeks of mismanagement. They are bleeding money from one of several business points, they are running low on funds and they have no idea how to simply stop the site without owing many people money. They made some cash, blew some cash and then got in way over their heads and every day in business gets deeper and deeper, so they bail and run with what they have.
A well run exchange can make $10,000 a week easily. That can become true within the first year. A small upper management group can drop $1000 per person in their pocket every week and never look back. That is not a rich man's job, but it is a pretty good paycheck for many and still leaves time for other investments. A poorly run exchange will lose money left and right and find the hole getting deeper and deeper, throw money at the fire trying to put it out and then not know what else to do but run.
I agree that an exchange should basically be a licence to print money, but there are costs that you have to consider, along with the slow start-up time as people won't send their precious Crypto to a new and unknown exchange.
Security: This is obviously the main thing. Many have tried and failed. You need to have an online hot wallet that covers what people will trade daily, but you need to have it 100% secure. That isn't easy. The cold wallet should be easier. If your exchange is just for Bitcoin, then it is probably not too tricky to keep everything up to date, if you accept lots of alts, I imagine that keeping wallets up to date would be a nightmare, often you have to manually add nodes etc.
Regulation: If you are in a first world country, the regulators are going to come and get you. You need to have a full KYC database, which is secure. You also have to follow the local laws for trading of currencies. Declaring your profits could also be tricky, especially if you don't convert to fiat. You will need a good accountant.
Trust: Are you going to be running the exchange 24/7? No. You will have to employ people to help you. They need to be technically proficient too, that might not be your friends and family. If you employ strangers, they will have access to large amounts of money, will they steal it? How do you know that they won't?
I personally woouldn't do it. Those that have done have run into problems very frequently. Now the remaining exchanges are more professional, but I still think we will lose some in the next few years due to the above mentioned reasons.