Yep. I have often heard "you are funny", or he/she is funny used as a compliment Oristar - I am not sure where you got the idea that it is normally derogatory. It CAN be - again it is all in the tone.
Not to mention those who, at least that I have met, used to jeer at others with the word "funny", let's see the definition of "funny":
(1) Causing laughter or amusement, e.g.
He has funny habit of blinking when talking with others.
(2) Intended or designed to amuse, e.g.
A funny joke.
(3) Strangely or suspiciously odd; curious, e.g.
It's a funny thing, but she put the ring on the dressing table a few minutes ago, and now it's missing.
There's sth. funny about the telephone; it won't work.
What can that funny noise be?
(4) Tricky or deceitful, e.g.
Don't get funny with me.
They had got together the whole evening, and I knew there was something funny going on.
(5) Sick, e.g.
She felt a bit funny.
So the word seems mostly a derogatory adjective, while the word "interesting" just means:
Arousing or holding the attention; absorbing, e.g.
An interesting story book for children.
In an interesting condition [situation].