If it was reversed and the bus driver had asked a Christian, "Did you know there is no God? Why are you wasting time with religion?" I am sure the atheists would consider it freedom of speech and worthy of admiration.
Yet the reverse is bad? That doesn't seem fair.
No bus driver should be bullying students with their personal beliefs/ideologies, atheist or otherwise. When a bus driver is on the job, you know, driving students to and from school, she does not have free speech protection under the law in her bus driving role. She is bound by the duties of the bus driver code of conduct, and the company that employes her can discipline/terminate her for violating their rules.
If that same bus driver wants to stand on a corner and yell at others about their personal sins, while off duty, that is protected free speech, assuming she is not violating any local or federal laws related to public gathering, etc.