Why Hermione wanted to bring their captives along Harry and Ron didn't quite understand, but she was determined. Somewhere in that mind of hers, they knew, was an explanation, a rationale that if they left Blaise and Draco, Voldemort would know where the locket had gone and would try to stop them. So they let her.
In the end they Stunned the two boys, and floated them along up ahead. Hermione told them that, given a few days, they could probably bring them around. And if they couldn't they could be sent to Azkaban, where they would be safe and sound.
Ron was suspicious. But he let her. He trusted her intentions. And more importantly, he trusted that she was right.