I've been tasked with writing a feasibility report on using the iPad in the college classroom. For reference, we're a small college (1,300 students).
I think the biggest disadvantages are a.)the inability to easily incorporate figures into your typed notes; b.)the lack of wireless printing; and c.)the relative scarcity of e-textbooks. Not having a USB port doesn't bother me, nor does the lack of USB. As of right now, the iPad is more secure in terms of malware and viruses (though I am willing to be wrong, and told I'm wrong, on this point). The fact is, most students don't care about network or personal computer security past making sure their machine works and doesn't get stolen. Removing the USB port removes a virus vector that's been particularly nasty on our campus. Making sure the students get just the apps they need helps the faculty in that the iPad, when used in class, won't be bogged down with distractions.
Now, there are a slew of other issues that must be considered (the students are allowed to buy other apps, music and such, will half of these end up in pawn shops in a week, do we have the capability to handle that many wireless connections at once), but there are a lot of advantages to the device.