Probably because she sees her husband rushing after the woman who tried to kill her and she puts two and two together and comes up with HELL NO?
I am 100 percent Team Regina and 100 percent Team Outlaw Queen forever and always, ride or die, etc., but we have to look at this how Marian’s looking at this: she was pulled through a time portal and sent 30+ years into the future. In Marian’s head, all she has to work with is what she knows from the Enchanted Forest. And back there, she’d been separated from Robin and Roland, presumed Robin was dead, helped Snow only to be captured by the black knights and used as an example as Regina threatened more townspeople and then she was sentenced to death, rescued by Emma only to watch Regina GLEEFULLY burn Snow White at the stake.
So yeah, I can see why she’d be pretty mad that Regina was now involved with her husband and son and even angrier when her husband rushes out after Regina. She’s in a brand new realm, 30+ years have passed for everyone else and she’s confused and scared and then she sees that? Of course she’s going to have issues with Robin’s life choices…which I’m sure will eventually lead to them realizing that too much has changed for them to be together or whatever the story is going to be…but for now, I think she’s justified in her anger.