This is because Voldemort believes that Harry is weak being an emotional person. Time and again, Harry had saved his friends and dear ones putting himself in danger. He had been sometimes foolish in doing so (like in the Triwizard Tournament) but mostly, he did out of love. Voldemort considered this a weakness and used it multiple times to put Harry in danger.
Beginning at the Chamber of Secrets, Harry endangers himself to save Ginny and in a way, the school. In Prisoner of Azkaban, he does spare Pettigrew's life. Now, when Voldemort was coming back in the Goblet of Fire, he would have had a good idea about Harry's weakness. It proved true when he saved Cedric's body (and other things he did in the tasks). Later Voldemort exploits this constantly to try and kill Harry. Had it not been for Dumbledore, Hermione and Severus, I think Voldemort would have succeeded.
So, obviously when Harry is not on the train, Voldemort assumes that he is gone either hiding to protect others or to find a way to kill Voldemort. It is most obvious that Ron and Hermione should be with Harry. But seeing from Harry's perspective, it is the last thing he would want - to hurt Hermione or the Weasleys as they were the only family he was left (and Lupin ofcourse).
Thus, Voldemort would have believed that Harry is gone for some reason and Ron and Hermione are gone looking for him. There is no reason for them to be together - as Voldemort thought he knew Harry completely.
This he must have shared with his Death Eaters and since no one knew better, they would have agreed to.