They do charge you again. The added charge isn't only for the glasses (which they recycle anyway), it's for the 3D presentation. It's a way for theaters to earn more money.
The 3D effect doesn't work for me, so I have to seek out a non-3D presentation of any film I want to see. All I see are double-images and blurriness with the current technology. It makes the films nearly unwatchable. If theaters go all-3D, I'll just resort to watching movies on Blu-ray.