It'll likely still work. Acrylic ones are just "gentler" because acrylic scratches easier than glass. What that means for you is that you might have to scrub longer since it's not scrubbing as hard, and may not have as tough of a scratching surface as the cleaners for glass.
For a small tank it shouldn't make that much of a difference. I would say that on both my old nano biocube, and on my new full-size tank, the Flipper cleaner has been a dramatically worthwhile investment, and makes it a LOT easier to clean the glass.