She misses him. She doesn't know when she is going to see him again. She probably expected him to always be there. She never thought they would be seperated, and when they were, it really hurt her a lot
Hermione is in love with Ron. He is leaving her and accusing her of choosing Harry over him, which is completely ridiculous. His judgment is impaired door the horcrux, and she may of may not realize this. Well, if the one u truly loved left u so coldly, wouldn't u cry as well? He isn't just another boyfriend to her; they are truly in love.