From the very first time we see them interact, there seems to be a cool, easygoing respect between the two of them. It isn’t until DNA Mad Scientist that we really can start to see the potential true friendship. She’s given his DNA, for frell’s sake!
That’s not to say they haven’t had their rough patches. The Way We Weren’t was downright BRUTAL on their relationship but it worked out okay in the end.
Aeryn is constantly there for Pilot, protecting him from everything that’s out to hurt him (including the other passengers and sometimes himself), and Pilot is a constant source of growth for Aeryn. I honestly believe its from him that she learned compassion - not that Pilot was particularly compassionate, but that through him she learned how to actually take care of another being.