What is the ruling on money earned from a father's work in a factory that uses pirated computer software, and is it permissible to spend it on studies, buying books, and paying university fees?

You are not at fault for disposing of the money your father gives you, whether by spending it on permissible things or giving it as charity. Your father's use of pirated software, even with his knowledge of its prohibition, does not make his earnings from his work in designing logos unlawful.