Yes — "not" is always capitalized in title case because it is an adverb.
"Not" is an adverb and is always capitalized in title case. AP Style, Chicago Style, MLA Style, NYT Style, and AMA Style all capitalize adverbs as content words that carry meaning in a title.
The word is only three letters long, but short adverbs are capitalized just like short verbs. The principle is grammatical category: function words like articles, conjunctions, and prepositions are lowercased, while content words like nouns, verbs, adjectives, and adverbs are capitalized.
APA Style, Wikipedia Style, and Sentence Case lowercase "not" in the middle of a title. Those styles use sentence case and do not distinguish between word types.
"Not" appears in some of the most famous titles in English literature. Both instances of "Not" in "To Be or Not to Be" are correctly capitalized as adverbs in Chicago Style. "Not" is never a function word and should never be lowercased in title case.
"Not" is a negating adverb and is capitalized in all title case styles. Adverbs are content words — they modify verbs, adjectives, and other adverbs — and all major title case style guides treat them as principal words requiring capitalization.