Like a lot of, something like 90% of functions not so much as a preposition as it does a premodifier. And premodifiers work like adjectives. They do not change the head noun, which remains the grammatical subject and still must be agree with the verb in number.
- People are coming.
Trouble is avoided.
- A lot of people are coming.
A lot of trouble is avoided.
- Ninety percent of the people are coming.
Ninety percent of the trouble is avoided.
- One percent of the people are coming.
One percent of the trouble is avoided.
As you see, you can remove the leading a lot of or the X% of, and nothing changes. Like adjectives, these premodifiers do not change the grammatical subject or influence the verb. The head noun does not change.