There was a thread a few weeks back about how to accomplish the transfer of images and I would say it was mixed at best. Many people expressed concerrns about "catching" the cable and pulling a camera onto the floor. Another concern was the camera battery dieing in the middle of a transfer. And with cameras that use CF (the T3i doesn't) there is a risk (although rare) of bending the pins.
The reality of the situation is either method works well but both have limitations. Some people have experienced issues when they have formatted the card in a reader; many of these issues involving computer literacy, in that the format (FAT16, FAT32, etc) does matter. It might even be worse with a MAC. If you transfer in the camera, then do a low level format, IMO opinion you are less likey to create issues.
Bottom line don't feel that a card reader is the preferred method, simply put it is an individual choice that should be based on how you use your camera.