they are the same quality, just one has a glass cover, and one does not.
Which you choose is really best decided by having a look, although if there was no matte option in the store, you are a little stuck.
Personally, I would always go with matte if given the choice, and would be wary about doing anything colour critical on a glossy display.
However, my macbook has a glossy (NB. NOT GLASSY) screen which i find very comfortable for day to day use.
Glassy screens on the other hand I find unbearable because:
1. too many reflections
2. screen brightness needs to be turned up high to reduce reflections, but then is so bright it is very uncomfortable on the eyes.
I will not be buying a mac with a glassy screen - ever.
Finally, lots of people do use them without issue. so horses for courses