Transistor Controlled 6x6 LED Matrix

So is the Arduino protected from the 5V supply?

Not sure what you mean, the arduino runs from 5V so it is a bit of a waste of time protecting it from 5V or else it wouldn't work.

If i upped it to 25V

If you connected that circuit to 25V it would not work because of the way you have NPN transistors switching the +ve power in an emitter follower configuration. These should be PNP transistors.
Also 120R is way too low to have as a base resistor.