Actually, it isn't. By definition, atheism is the -ism of Atheos (godless). That is, a belief in godlessness.
http://en.wikipedia.org/wiki/Atheism
The fact that atheism as a term predates theism as a term means that the alternative derivation (a-theism) cannot be correct, historically at any rate

Additionally the idea of implicit atheism (ie if you don't actively believe, you are an atheist) is a very new invention, and generally not very popular outside of atheists themselves.
Moving back to the subject of the OP, I'm not really sure what all the fuss is about. The bus driver objected to something written on the side of the bus (I support his right to do this, and would support it whether he was theist, atheist or whatever). His employers listened to his concerns, and between them they worked out a compromise solution (ie that the driver would only drive the buses with the adverts on if there was no other option) that both sides were happy to support. Sounds like a good victory for employer-employee relations if you ask me. Having said that, I would also have supported the company if they'd chosen to discipline the employee, or insist he had to drive the bus, just as I'd have supported the employee if he'd chosen to quit. Again, this support is irrespective of the actual views concerned.
No need for big drama or anything here from my point of view.