Actually, park hopper passes say right on them that they include unlimited use of the Disney transportation system, so yes, park hoppers do include use of the busses, boats, and monorails.
Disney not only does not mind if you visit resorts, it encourages you to do so. Not only are you likely to stay there in the future, but Disney makes money from people eating in resort restaurants and buying stuff at resort gift shops. Ya think the only people who eat at Chef Mickey's are people who are staying at Contemporary? No way! and that's the way Disney wants it.