SD Cruiser has a valid point, the majority of flights do arrive either on-time or close enough that you wouldn't miss a ship but there are some rare exceptions. Things can go awry on any trip no matter how you plan to travel. I wouldn't live based on fears of the exception but planning well is always a good idea.
On the transfers vs taxi, it's no secret on here that I'm not a big fan of transfers. Cab fare is usually equal or lower cost than the transfers and gets you to the ship faster without having to worry about waiting on that last lost bag or passenger that leave you sitting on the van or bus for long periods of time. Also, the more hands your bags go through before arriving outside your cabin door, the more likely a tag will disappear or your bag will end up at the wrong ship or heading back to the airport in the van with you on the ship. It doesn't happen often but I can't remember the last case of lost or delayed luggage I had associated with a cruise (not counting the airlines losing them) that did not involve a transfer. If you sail from a port a long way from the airport like Rome, Galveston or Port Canaveral the transfers are sometimes the only good option but for most ports a cab is a better option in my opinion.