No. Charles Xavier was sorry in that scene because he had just remembered the "Westchester incident", where one of his seizures hurt hundreds of people and even killed some. But the victims of that incident were (probably) random innocent people, not exclusively mutants specifically, much less all the mutants in the world.
The mutants are gone because Zander Rice developed some method of preventing mutants from being born, as he explained to Wolverine himself near the very end of the movie.