It's because in most of those sort of scenarios, we've got unlimited clean energy. If that's the case, pedalling doesn't make sense except for exercise. There are ebikes now that have a throttle alongside the pedal assist, so the size and weight of the bike is already low. Add the battery efficiency to get the 1,000 mile charge, and you can use the throttle to get everywhere. You'll get there faster too. If bikes show up in sci fi, they're likely to be electric motorbikes.
In a future with clean flying cars, especially the post scarcity future, the vast majority of the current problems with cars are gone. You just book a self flying car to take you to your destination and back, and it goes to another customer when you're done. In a Star Trek type future, you just beam there and back. For the most part, people don't care about travelling, they just want to be at their destination. If there's a hand wavy sci fi way around it, people will take it.
The problems that bikes and ebikes solve at the moment tend to be solved in futuristic stories, or in post apocalyptic stories, they don't matter. Why bother worrying about pollution when you're in a nuclear winter?
In the real world, ebikes are great, but in futuristic stories, they generally don't matter.