Well, it's mostly little things. Just personal preference really. Adium is horrible about reconnecting on wake from sleep on my iMac, while Proteus works perfectly. Adium is buggy when it comes to meta-contacts and contact groups, Proteus is not. Proteus handles file transfers better (not perfectly though). I personally like Proteus' interface better. The way you turn on/off individual accounts is easier in Proteus. There are more little things like that.
On the other hand, Adium is more customizable than Proteus (Proteus is customizable though).
They're both free, and they're both open source. In the past, Proteus was not free, and it was closed source which turned a lot of people off. Now that has changed...