It is mentioned that Buzz Lightyear had known Bonnie way back when she was a little girl, and it would explain his shock while he sees her after at least ten years. However, because of her father and his obsession with avenge on the Space Ranger, Bonnie Lepton complies with her father simply because he is just that -- her father. But just because her father is slightly crazy doesn't mean Bonnie is.
During the episode "Eye of the Tempest", she starts to see a different point of view, and ultimately realizes that her father's obsession has gone too far. Thanks to Bonnie, Team Lightyear stops Spyro von Madman from overtaking a power plant and gathering more power before he could destroy anything else.
In the end she is seen supporting her father, who is now free from the crystal's corruption.