I wear boots all the time. Grip on the deck is much better. It's warmer. My feet are protected from rocks and shells and stuff, and from chafing from the straps.
My all time favourite boots are the Neil Pryde Low Cut Round.
http://www.npsurf.com/products/protective/boots/origin/origin-lc-round.html They're high enough that you can tuck your wetsuit legs into the top, but low enough that they dry quickly and don't look too naff with boardies.
The new high end Mission models are not as good because the ankle is too low cut.
The worst thing ever is getting shells inside your boot. It's really painful if they get between your toes and a bugger to get out. The cause is standing flat footed in the shore break allowing the wave to bag your boot and let the sand and stuff get in. You need to do a little hop so your feet are not on the bottom when the waves hits.
Avoid split toe boots. They tear in about a week. Round toe or internal/hidden split toe is fine.
Also avoid very low cut reef shoes if you have to walk across a sandy beach. Sand and crap gets in no matter what you do. They're fine if you walk across a ... reef.