Atoms are fine processors, very low power and therefore generate very little heat.
The low cost is because they're not very fast compared to a modern CPU, also the low end/cheap motherboards have very few expansion options. The chipsets are also old.
If all you want is a low power file server, an Atom is fine. If all you want is a "nettop" i.e. a desktop version of a netbook, just to browse the web and write some documents, an Atom is also perfectly fine.
The only reason not to get an Atom is if you want computing power, they're not designed to handle any intensive tasks.
Hope this helps.