Both are incorrect, but if you inserted the word "the", the first one would be correct, while the second would still be wrong:
(1) Why is the past tense not used? (correct)
(2) Why is not the past tense used? (not correct)
"Not" modifies "used" rather than "the past tense": "Is the past tense used?" "No, the past tense is not used." Adding "Why" to the beginning of a sentence pulls the auxiliary verb into second position, but leaves "not" and the other words where they were.