Toffee’s relationship with sonic is one of blind trust, betrayal and hero worship.
Because Toffee was the leader of the freedom fighters/resistance to GUN and Eggman 8 years ago, Sonic was aware of her as a child, she was a hero and inspiration to him, not knowing much about who she really was. He imprinted his own morals onto what he imagined her as until she “disappeared” 8 years ago.
Years later, when Toffee breaks out of prison, where she had been in cryo freeze for 10 years, they eventually met.
Toffee was initially entirely indifferent to him, and Sonic was very open about his childhood idolisation of her, even claiming to have her (wanted) poster on his wall as a child.
Hearing and seeing Sonic’s fight against Eggman and GUN endeared Toffee to him eventually, and she took up the role as a mentor figure that he wanted from her. She saw a kindred spirit, at first, in him.
However, it was all false idealisation, and eventually Sonic found that his perception of her was entirely self-imposed.
Sonic later feels very betrayed by her, when her more extremist views and actions came to light.
While Sonic wants to stop Eggman and protect his friends, Toffee sees no action against Eggman or GUN as “too far”. She’s an extremist and an eco terrorist, who fully believes that drastic action is the only option left (especially after seeing how devastated the natural environment has become in her absence.)
When Toffee reveals her actions and plans, which involve the belief of eradicating humanity as they are a blight on nature, to Sonic - by acting and letting him find out what she’s done, he feels betrayed and turns in her. She feels this is tragic, that he should have been the one to see things her way, but ultimately she is not betrayed by his turn against her as she never saw him as a friend, an admirer. She accepts he is now her enemy.
Sonic wants to stop Toffee’s plans, but thinks he can reach the same goal without resorting to terrorism, where as Toffee believe he’s ignorant and will see things her way eventually, now believing she can convert him.
She does truly respect his goals, and respects how kind he can be, but she will not falter on her ideals.