What is to stop an exchange from not paying you other than potentially risking loss of users and business? With the volume MT GOX does it could be quite profitable to just close up shop and walk away with the Cash and Bitcoins. I don't see what could stop this from happening with the cash scenario, although I am not sure what is digitally possibly regarding the bitcoins siince they are the ones making the trades between two parties. I guess this question has to do with the mechanics of how the coins are being traded on their end.
this is not a problem unique to bitcoin. have you ever heard of bernie madoff? mf global?
to protect against this, there are laws requiring segregation of customer's funds. this should be something easily verifiable (though this week's discovery that pfg best's ceo had stolen these segregated funds shows even those laws don't eliminate the risk of losing money to fraud).
the general advice is to never store with an exchange more than you can afford to lose. consider which jurisdiction the exchange is in and how difficult it is to even participate in trying to obtain recourse if there is a problem (see the bitcoinica mess as an example).
with bitcoin being something you can store securely yourself, you can lessen the chances that a major problem at an exchange becomes a major problem to you.