It's you, not Tom, who is/are to blame for what happened.
The model answer here is "is". When I search for the reason, I come across a rule as follows.
If your sentence compounds a positive and a negative subject and one is plural, the other singular, the verb should agree with the positive subject.
The department members but not the chair have decided not to teach on Valentine's Day.
Then I am totally confused. Why does this rule contradict the model?
In English you can be plural. When a addressing a group of people one may refer to that group as you. The word you can also be singular, used to address a single person. Your sentence is missing the context necessary for a definitive answer. It could mean either.
It's you [a group of nine people], not Tom, who are to blame. Here we have nine people in a group being addressed by the speaker as you.
or
It's you [Maria], not Tom, who is to blame. Here we have one Maria and one Tom.
Without knowing who your you is we can't say which option is correct. Outside of a quiz question, however, your use of is or are will provide contextual clues as to whether your you is singular or plural.
The model is wrong. The correct sentence is
It's you, not Tom, who are to blame for what happened.
The subject of the sentence is 'you'. The verb must agree with the subject of the clause. The correct second person singular form of 'to be' is 'are'.
You are to blame.
This is such a common mistake, even among native speakers, that many people don't even know the difference.
