I don't see it as being any different from any other vanity plates.
Around here you can get license plates depicting organizations you belong to, or the logo of your favourite sports team, etc. That's not a case of the state showing preference to these organizations, but rather allowing residents to express themselves in another way.
Here is a page showing all of the different graphics available for Ontario license plates. While Christian plates aren't depicted, I really don't see how one could argue that Star Trek license plates are okay but Christian ones aren't.
I don't think a plate that's captioned 'In God We Trust' is any worse than all of your currency that says precisely the same thing.
EDIT - It is of course a different case if these plates are mandatory.