Before the diatribes on stuff, and someone will post some AIM crap and some stuff from the Air Traffic handbook, I'll throw this out there.
Your CFII wants you to learn to communicate without saying it, do it.
Now, that being said, I use "Roger", "Affirm", "Wilco" and "Charlie, Charlie" under certain circumstances.
In the states, I almost never used any of those terms, as most stuff you discuss requires a full readback (even in NYC airspace - yes, I'm that guy if they were giving me a clearance that I didn't recognize).
Things like "Position and Hold", altitude and heading readbacks, you really want to get the readback, and you understanding the instructions out in the open.
When you get bogged down in a communication break down ("SpamCan123, recleared direct Taylor, direct Docampo, I95 to five0" "SpamCan123, recleared direct Taylor, direct Docampo, I95 to five0? Correct?" then the controller repeats it, then you repeat it then they repeat it.), just say "Roger", "Affirrm"
If you are flying in regions that are not the US or you're using HF, sometimes that's all you can get across that you understand.
So there. My un-supported position on the use of "Roger".