Is the phrase neutral, like "you need to know", or it has some negative connotations?
Context, context, context.
If you suspect that your hearer does not know X, You have to realize X is informative: it means "I tell you X because it is necessary that you know it*. In this case, it is more or less equivalent to You need to realize/know X.
To understand why he is doing it that way you have to realize that he has very little training.
If you suspect that your hearer does know X, You have to realize X is a reproach: it means Surely you know X—why are you ignoring it!.
Why are you just standing there? You have to realize that a horde of angry orcs is about to descend on us!
Note that You need to will not bear this meaning.