It's also coming off the back of the entire series of Miyuki never telling Sorata straight-up what she thinks of him.
She says she's choosing Tokyo. To what end, though?
Plus, Sorata's mocked and belittled and derided by their classmates, by her acquaintances, by her brother--even Mary was insulting him when she first entered the storyline.
And through it all, Miyuki never stood up and called those people out, or directly expressed how she feels about Sorata. He doesn't even know she still has the ring he made her, because she hides it on a chain around her neck and never told him.
Sorata's done what he felt he could to show he wants to be with Miyuki, and she's never met him halfway in a manner that isn't roundabout or indirect.
And that's with Ayano's mindgames that have screwed with Sorata's head since they were children. all Miyuki said was that "he always says unnecessary things". But that's it. She doesn't call it "mind games" or reflect on how Sorata wouldn't "get" all her Kyoto dialect mannerisms, and it would seem she's never noticed how troubled and anxious he'd become over time because of it all.
Sorata's not perfect. But his call here is based on the fact that he's all but convinced, after years of trying to tell himself otherwise, that Miyuki is only with him because of their grandfathers.
And even here--all Miyuki said was "going to Tokyo was my choice", and "adding onto that, I interpreted grandpa's words as 'go to the same school as Sorata'".
That is not the same thing as saying "I want to go to Tokyo because Sorata is there and I want to be with him".
It's the same story from chapter one. Miyuki can't bring herself to state her feelings outright, and it's compounded into Sorata feeling like she's with him out of obligation and he can't stand her stifling herself.
Unless I missed a chapter, Miyuki's given him no reason to think otherwise.