Two words: "counterparty risk".
replies(1):
Essentially conterparty risk is the risk that the other party to a contract, in this case the broker, defaults.
Bacause automated arbitrage trading requires you to hold your funds with the broker, rather than transferring them to your own (preferably cold) wallet, you are exposed to the risk that the broker goes out of business without returning your funds, or otherwise fails to live up to its side of the bargain.
With crypto-currency exchanges, that risk over the long term might be assessed to outweigh the possible rewards from arbitrage trading.