'I don't like you because you have money', this sentence is a little logically weird for me, though I know it conveys the same meaning of the sentence 'I like you not because you have money'. Can I directly say the second one instead of the first?
From my point of view, both sentences seem unsuitable. I suggest this sentence: "Money is not the reason that I like you". I just guess the meaning of your sentences. Hope that it will be correct per your intent.
They mean different things. In:
I don't like you because you have money.
"you" has money but isn't liked by "I".
I like you not because you have money
is more of a sentence fragment or at least an incomplete thought.
I like you not because you have money, but because you are kind and considerate.
Without the explanation, you could also use:
I like you but not because you have money.
In either of these examples, "I" likes "you", but the reason is not the money "you" has, but another reason.