In more simulation-focused games, cycling and walking paths are often available, and you can use them, but they come with many of the same constraints they face in the real world. In practice, that means they are usually not efficient as the primary way to move large numbers of people across a large city.
Reading your comment, it sounds like you want a game that is realistic in most respects, but treats transportation differently, in a way that makes your preferred options the optimal strategy. That is going to be hard to find, since transportation is a core part of city-building sims, and developers tend to pick either realism or a more utopian/fantasy model rather than mixing both in a single game.