I understand your cynicism. I was just like you. But trust me, it's not necessary that you have to have other motives, you can really be genuine and sincere about your compliment. I do not actively work on trying to compliment people. The only thing I have changed is that if I have something nice to say to someone, I don't held it back anymore.
I think the core point that divides creepy/suspicious compliments and genuine ones is your motivation behind them. If you're searching desperately for something nice to say to the girl at the crosswalk because she has great cleavage, it's never going to sound sincere, and she will pick up on it.
However, the exact same compliment delivered out of a motivation simply to put a smile on someone's face can go a lot further. I used to wear quite quirky clothing and getting a compliment on my wardrobe choice would make my day. When I give someone a compliment, that's what I'm trying to achieve - I'm not trying to make myself feel good, or get in their pants, I just want to pass on some of the good will and good feeling that has come my way in life.
After a lot of travel to places where salesmen and conmen are pretty bold (like Turkey and India) I've gotten to where I'm fairly comfortable saying "no" to people asking me to do things I don't want to do (including "loan me a few bucks" or "come look at what I have to sell; it's not far", and so my fear of interaction and cynicism has gone way down. I can get out of it (and still be smiling), if I fall into a conversation I don't want.
If I look friendly and safe (i.e., playing w/ my 3-year-old on a NYC street) strangers talk to me, and it's pretty clear they aren't after anything.
So from the POV of the complimenter -- agreed, some people will be suspicious, and that's fine. Give your compliment, and keep walking so they know quickly that's all you were doing, and maybe they'll be a little less fearful next time.
Complement someone when you're introduced, or meet for some purpose. Complementing people you pass on the street seems pointless.