Each exchange carries a different risk profile and also has different features. For example, Gemini and GDAX are highly compliant. They are licensed wherever they operate. After the BTC-e takedown in July for money laundering and unlicensed money transmission, this is relevant. They are considered the safest US exchanges for that reason.
But they also don't support many coins for trading -- just BTC, LTC and ETH. That's why people turn to exchanges like Bittrex, Kraken and Poloniex. Altcoins are the main reason why all these exchanges exist. The ones you mentioned are the upper-tier exchanges. There are all sorts of small exchanges like Mercatox and Novaexchange which specialize in new and low-market cap coins.