I agree with Bill and Eric, in that user error associated with managing multiple cards is probably a more likely "failure" than a good brand name CF card outright failing. Anything is possible of course.
I've used over a dozen mostly Sandisk cards for almost 9 years now and never lost an image or had a card fail. Maybe just lucky.
I always use a card reader although I suspect using a USB cable is "safer" to the extent that it eliminates the potentially expensive problem of bent CF card pins in the camera. I've never bent a pin but I've read more than a few stories here. Probably "user error" but it happens.
Repeated inserts of a USB cable could similarly stress the camera USB port, which is also an expensive repair. But that port is arguably less critical than the CF pins (??). Lots of ways to call that.
I recently bought a 16GB card because periodically I was using well over a half dozen cards in a single day, and I did not like managing that even though I have a system. I otherwise have 8x4GB cards and 4x8GB cards. So I still use multiple cards for a few regular shoots a year but I like the fact that a single 16GB card gets me through most daily shoots. That with 12mpx cameras.
Interesting discussion re SD card reliability. That is an important consideration with the new Nikon "paradigm" that is more or less forcing many to SD cards.