A few questions.

[Ludens]

Do the colleges currently serve a purpose in the game? I haven't noticed any effects between leaving my new family members in the backwater ends of the empire and sending them to rome to learn in the... highest form of school.

Yes, they certainly help your generals develop good traits, especially when compared to leaving them idle in a governed city. For example the very useful logistician trait can be acquired at an academy. However, your generals also learn from practice so even without an schooling, so they will do quite as well if you just keep them occupied. Logistics can also be learned in the field.

Is there any recommended tax setting? Even on low I'm having problems keeping people happy, and I thought the one that balanced it all out was high?

I don't think there is such a balance. You should use the one that leaves the people happy (green face) with a minimal garrison.

Is there any factors that can cause a lot of unrest? One town doesn't have many health problems, and its only a short distance from the capital, but it has huge unrest problems.

Governor's trait and the presence of brigands. Also a recent occupation will cause a lot of unrest that slowly dies down.