Without getting into the politics of it, the purpose of the air strikes according to NATO to "to halt and reverse the humanitarian catastrophe that was then unfolding."[1] - specifically a "ethnic cleansing campaign"[2]. I think it's possible the pilot or others to feel they're there for reasonable reasons, even if they don't hold any particular ill will towards the guy on the other side.

[1]https://www.nato.int/cps/en/natolive/topics_48818.htm

[2]https://www.nato.int/kosovo/history.htm