-S is for reciprocal action: vi ser - we see; vi ses - we (will) see each other.
More examples of reciprocal -s here: http://www.thelocal.se/blogs/theswedishteacher/tag/reciprocal-verbs/
Because the other person will see you too. Like samulili wrote above, "we (will) see each other" is the literal translation, but in English the phrase used is "See you". Languages tend to have these colloquial phrases for common expressions, so they will not always translate literally.