Either of them can be used here, by saying either of them you're basically saying the same thing but they do have slightly different meanings.
"Wouldn't it be better if we went there by car?" - This sounds more like you're thinking out loud about the idea of going there by car, and that you think it'd be a better way to get there.
"Wouldn't it be better if we go there by car?" - This is a more direct suggestion of "We should probably go by car instead". Although a more accurate to say to say it would be:
"Wouldn't it be better to go there by car?"
Saying either one sends the exact same message and it doesn't really matter which you use, but that's the slight difference between them.