Wells uses sort of bad physics to explain this one...
The Time Machine moves through all four dimensions at once, it creates its own kind of temporal space field around itself which is kept up as long as it keeps moving. It doesn't 'travel' through normal fixed space so that's why it doesn't just crash and explode when the bomb drops.
Wells also uses a lot of other bad physics and biology (Nevertheless accepted at the time, this
was the very first science fiction book after all). He's almost as bad as the writer of Jojo for it.
It#s still an absolutely fantastic book though, especially the horrific monster crabs in the final chapter.