One reason is simply because so much of the space is already built up, which means building anything new usually requires destroying a whole lot of stuff already there. Despite the challenges of obtaining cooperation from affected people, the alternative is worse: simply ousting people by force. That's what the government usually does, and it causes problems, because now large swaths of the population -- black people, Hispanics, the poor -- hate both the government and mass transit. They'll fight back as best they can, and they certainly have a right to defend themselves.
Howbout this: for every housing unit destroyed, the city has to build two affordable housing units, and everyone whose home is destroyed gets the option of living in one for free, to make up for the imposition. We could also take this opportunity to build housing immediately adjacent to mass transit. There would still be protesters, of course, but they would get drowned out by all the folks stampeding toward the free housing. It would be expensive, but it would be popular and it would get done.