Learn Croatian: Zašto niste unutra? - Why are you not inside?

For the verb 'to be', you cannot just put ne in front of the normal verb. The negative word ne and the verb ste (you are) merge into a single new word: niste. Saying ne ste is always incorrect.

Where is the word for 'you' in this sentence?

It is hidden! In Croatian, the verb form niste already tells us exactly who the subject is. Because of this, you do not need to include the actual word for you (vi) unless you really want to emphasize it, as in Zašto vi niste unutra?.

Am I asking this question to one person or multiple people?

It could be either. niste is the plural form, so you use it when talking to a group of people. However, Croatian also uses this exact same plural form as a polite way to address a single person, like a boss or a stranger.

Could I put niste at the end of the sentence, like Zašto unutra niste?

Technically yes, but it sounds unnatural here. In Croatian questions, the verb usually wants to be in the second position, right after the question word (Zašto). Keeping niste right after Zašto is the standard and most natural word order.