I think Cassie is totally clueless when it comes to Ennis. She says it herself at the bus station: "I don't get you, Ennis del Mar." She doesn't know that Ennis loves Jack; she just knows that Ennis doesn't love her.
Clearly, Cassie was in love with Ennis and wanted to be his wife. Ennis broke her heart when he stopped all contact with her. She never got an explanation from him. She had no idea why he suddenly stopped calling her and ignored her notes. I think it was an awful way to break up with someone, especially since both Ennis and Cassie lived in the same small town and were bound to run into each other at some point.
But getting back to your original question, no, Cassie was not homophobic.