They are fine, air flow is generally handled through the vents on the sides/bottom of the case, and expelled through the back vent.
I've been using one on my Macbook since 2012, no issues. I would recommend getting a TPU (Thermoplastic polyurethane) one over a silicone one though. Working at the Apple Store I've seen a ton of the silicone ones that seem to react with the plastic under it to form little puddles of what looks like Oil all over the keys. Plus, the silicone ones are thick (more likely to make smudges on the screen) and they stretch (eventually stop fitting that well on the keyboard.
That uppercase branded one that csurfr recommended is a decent one. I have that one myself. Hope that helps!