Is it permissible to pray alone when the morals of the majority of those praying are bad?

Do not abandon the mosques of Allah due to ill-will towards Muslims. If the people of the mosques are ill-mannered, then who would be well-mannered? Rather, it is obligatory to advise those who fall short and to call the wrongdoers with wisdom and good counsel. It is not permissible to abandon prayer in mosques because of the mistakes of others.