When because follows a negative construction the meaning can be ambiguous. In the sentence he did not go because he was ill, for example, it is not clear whether it means either ‘the reason he did not go was that he was ill’ or ‘being ill wasn't the reason for him going; there was another reason’. Use a comma when the first interpretation is intended (he did not go, because he was ill), or avoid using because after a negative altogether.

  On the construction the reason … is because, see usage at reason.