IB is a bit unique with their Universal account. If you are not actually in a futures position, they roll all cash into the same accounts as the other asset classes, and this is protected. They also have third party insurance of funds, etc.
A straight up futures account is not protected, but in terms of safety, there are no worries except in cases of fraud. If a firm goes under, the accounts are passed to another firm by the NFA. In fact, since the current system went into effect in the '70's, no one has lost a single penny from a futures firm going under. This is a direct quote from the chairman of the CME a few months ago. I got it from a SFO magazine interview, but was something I already knew. This is why funds are segregated. In cases of fraud, where the funds were not segregated, you are screwed, and the officers at the firm go to prison. This actually happened to me years ago at a firm called FuturesWise Trading. Full on case of a guy who ran an IB (not to be confused with Interactive Brokers), just flat out took customer money, and used other customer money for payouts to clients (Ponzi scheme). His name was Snively, and he was just recently released from prison. The scary thing is I checked him out with the NFA and CFTC and he was golden, but new. Stay with the major FCM's, or IB's that clear through them and you will be fine.
BTW, in the Refco meltdown, only fx traders got screwed, not futures traders. Forex has no protection whatsoever.