My biggest problem with bitcoin is there is no legitimate company that can be entrusted with alot of BTC because like others said the problem is security because most of these websites got hacked and sometimes we need to wait for 30 minutes in order for the transaction to get 1 confirmation which is annoying for me.
Why considering that cases as a problem.
If you are talking about exchanges sites there are some ways and good practices if you are planning to do some exchange method and besides it really makes sense to have an exchanges in multiple exchanges rather than in a single site disregarding the rates.
If you are talking about bitcoin investment (HYIP, Ponzi etc), then it's obvious, stay away from that kind of site.