Using 'presume upon' implies disapproval of someone's behavior, usually selfishness or rudeness. I cannot believe she would presume upon our goodwill like this.
Pro Tip 2/3
Implies Expectation
'Presume upon' suggests an expectation that others will comply with the presumption. He just walked in and presumed upon my help without even asking.
Pro Tip 3/3
Not Always Negative
Sometimes 'presume upon' can imply initiative in informal settings; the tone is key. She presumed upon the team's agreement and led the project to success.