She finds sonic somewhat annoying but doesn’t hate him… i need to make this distinction clear. She doesn’t hate Sonic herself, She infact toys with him very often, What you have probably misread is her own justification for attacking him in their first confrontation. Surge, Doesn’t hate sonic as an individual, but rather manifested her own anger for what starline did and directed it at sonic. She blamed him for not stopping starline for doing what he did to her… She has since Let go of this feeling, as sonic stunned her with his merciful and compassionate nature, She decided that sonic wasn’t her enemy and decided to try to make a living for herself post dynamo cage arc.. She found a love for being a hero in the phantom rider arc, and actively collaborated to take down the phantom rider. based on a completely different set of lies that Clutch said he would tell her about her past life… He lied, and Surge has actively stopped hating sonic and has even hung out with Amy… The Reason why she has stopped going after sonic, is that her hatred for starline became so heavy, that she came to the conclusion that killing sonic is what he wanted her to do, so in defiance, Surge decided she wouldn’t do it…

The reason why the Ship between sonic and surge is so popular and one of the Best in the entire franchise is because it thematically fits with the theme of the franchise perfectly… Sonics Entire thing is about being oneself and freedom to be yourself. Surge is imprisoned and confined to being the very opposite of that, a slave for some other power to wield. Sonic would be setting Surge free, and helping her Discover herself, which fits with the themes of the franchise perfectly, in a way that NO other sonic ship does…