Because in English, "where" can mean not only "in or at what place" (sense 1) but also "to what place" (sense 5): http://dictionary.reference.com/browse/where , especially in combination with "go" - so "Where are you going?" is the usual question.
(There is an old word "whither" which specifically means "where to" which could also be used in this connection, but it is all but forgotten.)
So English speakers often have difficulty knowing when to translate "where" as "nerede (wo, kie, ...)" and when as "nereye (wohin, kien, ...").
What you state is not incorrect. The ye in nereye gives you the impression that you are trying to get somewhere. In other words you are not there (nerede). This is why nereye is just where, as opposed to where to. Unless, off course, you are using a one-liner 'nereye!' = where?,which I am sure is occassionally used in Turkish when one is familiar with another.
Gideceksin = you will go. Şimdi gideceksin = you will go now. Will you go now = şimdi gidecek misin. However, nereye turns a statement into a question şimdi nereye gideceksin = where will you go (to) now. In English, the (to) makes no difference, but for the sake of nere(ye) you add the to for direction.
"Sen şimdi nereye gideceksin?" Translation: Where are you going to go now?
Why isn't this "Where will you go now?"
I cannot see by not using "to" in your answer, it is wrong?
Şimdi - "now"
Gidecek - "to go" + "-sin." - "You."
Nere - "where" + "-ye" where to?
Nereye? - "where to?" - I think this the answer to your question.
Where will you go to now? - Correct.