Is it permissible to benefit from money earned from a scientific website that displays free books and references which I do not own, and 98% of the website's profit comes from advertisements on the pages of these books?

It is not permissible to publish copyrighted books for free without the permission of their owners, because that constitutes an infringement of their rights and a disregard for their financial entitlement. The high price of books does not permit their publication except with the permission of their owners. As for earning from advertisements on the website, it depends on the type of advertisements: if they are permissible, then the earning is permissible; but if they are forbidden, such as gambling, usury, and obscenity, then it is not permissible to display them or to earn from them.