The problem with BTC right now is that many businesses are operating without guidance or oversight. Financial companies in the United States and abroad are audited by third parties to ensure that the operators of said companies are behaving ethically. Their financial records are audited as well, and in the majority of cases this prevents misuse of consumer funds.
Sites like MTGOX operate just like a financial institution, but lacked any of the oversight seen at financial institutions. This allowed them to lose / steal their customers' money, possibly over the course of years without being noticed. Personally, I think MTGOX was running a Ponzi scheme for a very long time. This would likely have been noticed by auditors very early on.
Fact is, most BTC companies are run without oversight today. I would say that certain companies, such as Coinbase, are likely subject to more oversight than others on the market. Therefore, if you do your research, you can find companies which are more trustworthy than others. BTC-e has been around a long time, but really has only been a high volume exchange for about 2 years. In the Bitcoin world, this may seem like a long period of time, but in the business world it is not. BTC-e also lacks transparency on their ownership.
Bitcoin at your own risk. Nothing beats the security of a well-defended computer with your own Bitcoin wallet.
