Dictionary.com top 3 definitions for prejudice:
prej·u·dice [prej-uh-dis] Pronunciation Key - Show IPA Pronunciation noun, verb, -diced, -dic·ing.
–noun
1.an unfavorable opinion or feeling formed beforehand or without knowledge, thought, or reason.
2.any preconceived opinion or feeling, either favorable or unfavorable.
3.unreasonable feelings, opinions, or attitudes, esp. of a hostile nature, regarding a racial, religious, or national group.
So no. Isn' it prejudice to say "I believe in God and this is why." Therefore, it isn't prejudice to say "I don't believe in god, and this is why."
Prejudice would be "I don't believe in god, therefore I hate and would never hire a religious person."
or
"I believe in god, and therefore hate atheists/agnostics and would never hire one."