Species 8472 had every right to regard Voyager as hostile and as a threat.
During their first encounter Voyager attempts to both tractor beam the bioship and beam it away. Both hostile acts. Then they board it as if they had every right to. The pilot had every right to regard them as hostile and attack. Possibly consider them in cooperation with the Borg even too.
During their second encounter the Borg are actively protecting them. It's only by this point that Kes has established any kind of telepathic communication with them. Before this Kes just had a premonition of dead Borg and "Voyager's destruction" and she didn't foresee Harry getting hurt until they had already boarded the 8472 ship. So they had already proven themselves hostile by that point and the vision of Voyager's destruction, well that didn't come true so how reliable was it?
During the 3rd encounter, Voyager actively invades their realm and uses biomolecular torpedoes to destroy a bunch of their ships.
So yeah, Voyager was really the hostile power here. The most provocative thing 8472 did was defend themselves and have the gall to counter attack aggressive forces crying out "the weak shall perish!" which could just be a battle cry for all we know. Given they were perfectly willing to stand down despite all of this in In the Flesh, proves them to be reasonable.