The title seems pretty basic to us: The Time Machine gets its title from the Time Machine invented by the Time Traveller. Without the Time Machine, there is no story of time travel. We suppose the same could be said of the Time Traveller, though: without him, there's no Time Machine in the first place. So why give top billing to the invention rather than the inventor?
Let's also look at that subtitle: An Invention. Certainly the Time Machine is an invention – it's a new machine that the Time Traveller invented. But "invention" can also mean a lie or a story – something you just made up. So, if both a machine and a lie can be described as "inventions," the title here may remind us that the people in this novel don't entirely trust the Time Traveller's story. Or maybe it's a reminder to us that the whole thing is just a fictional story that Wells wrote.