A MacBook Air gets hot, just like any other laptop, although 100°C is relatively hot (if not, almost the maximum a Mac can handle).
There are reports where users complain about their temperature flirting with 100°C, so you're not alone.
Things you can do to prevent getting the Mac too hot is making sure you haven't covered his ventilating holes. Place it on a flat, hard surface (no lap, pillow or blanket as developers tend to do. At least, that's what I do once in a while :-)).
Other things you can do is make sure you don't run too much applications at the same time, or you could use a laptop stand to get extra fresh air under your Mac.
Or if it's really bothering you, you can always invest in a professional laptop cooler.
What you should keep in mind is the MacBook Air will shut itself down when there is any chance of damage. So you've got nothing to worry about. Your Mac won't get harmed.