There are a few technologies being developed to keep them honest {Smart contracts} And also making them more transparent. With MtGox and some more failures on exchange levels, a lot of the spotlight was shine on them.
You will also see regulators putting a lot of pressure on them, to be honest one of these days. And this is not only a problem with crypto currencies, it happens with fiat exchanges every year too.
MtGox will not be the last, we see of scammers at exchange levels.