Why wouldn't 8472 be hostile towards Voyager? First contact was their away team strolling into their ship as if they had every right. Only then did the 8472 start aggressively coming at them. Entering someone's property is going to provoke a hostile reaction from most people.
The second time they were with the Borg who were very obviously covering for them. Why shouldn't they have assumed they were the enemy then? By that point they were. Janeway didn't even try and negotiate with 8472, she just made assumptions. I always got the impression that 8472 decided to "purge" the galaxy once they realized it wasn't just the Borg coming after them but the Federation too.
Bull.
If Species 8472 were telepathically linked with Kes, then they knew from reading her mind that Voyager and others in the galaxy weren't hostile toward them. Janeway also told Kes to tell them they weren't their enemy and they meant them no harm. 8472 ignored it. Janeway did try and open up negotiations with them. First Contact was made thru Kes, not from entering their ship. It was 8472 that made assumptions, not Janeway.