it's actually not annoying at all. it's just where they are. i would find it more annoying if they still came out of the side.
the main downside is that they are rather second-class citizens in terms of usb ports, being quite slow, and very weakly powered. an input device would be fine, the tablet, say, but anything resembling file transfer gets a bit tedious - ipods, external drives, scanners, digicams etc
Dual 1.8GHz G5 2GB, 1TB, Radeon 9600XT 128MB, 10.5
20" Apple Cinema Display + Dell 2005FPW 20" dual-head
iBook G3 700MHz 640MB, 40GB, Rage128 16MB, 10.4, dying battery