I have a manual transmission and I notice a slight whine.
I never thought it was something to worry about and I still don't..
I used to have a civic that on occasion whistled or had a high pitch whine, and I traced the noise to the air intake (well, I stopped when I got to that point). Had the problem for years. I ended up selling the car at 190k miles and the new owner didn't have any problems with it.
I don't think I would worry about it.. But if you want to search for the noise, check the air intake, as it could be channeled through it, and would explain the variable pitch increasing with engine RPM's, as it sucks more air into the engine..
2007 328i, Montego Blue, R.I.P.
E.D. Planned for Fall of 2011....