Joyce sees a different Buffy from the rest of us as well. With the notable exception of the attack on Buffy's school, Joyce sees Buffy who is so irresponsible that she can't even pick something up for a mother at the mall without being distracted by a cute boy within moments who then completely forgets (and also wanted to buy a dress that makes her "look like a streetwalker" to which Buffy replies, "But a thin streetwalker"). She doesn't see Buffy going out to save the world, but going to the Bronze (heh, just remembered when Joyce asked if boys would be there and Buffy snarks something about it's where the nuns hang out). Since her arson of a gym and saying it was filled with vampires, Buffy can't even stick with cheerleading anymore. Joyce sees her house is a mess more often than not (like from when Xander and Cordelia are attacked by Bug Guy), which she'd assume was Buffy. God only knows what Snyder told her.
I don't blame Joyce for not trusting Buffy's judgment at all, based on what little she knows and how much she misunderstands based on her limited knowledge and context. ('Course ignoring bloodstains on Buffy's clothes is another matter, though I suppose that doesn't help either.)
That said, Joyce does seem more concerned about the sexual element than about the dangerous element involving Angel. I don't understand that tendency of hers to not see what she doesn't want to see until forced to, so I don't know. Maybe Joyce focuses on the sexual aspect in order to avoid the much more scary thoughts of Angel being a dangerous stalker saying things like, "I'll die without Buffy, she'll die without me." That is, she can't stand the thought of Buffy being killed, so she instead focuses on something that doesn't threaten that possibility.
