Basically because "reversion to the mean" does not really apply here. Cities certainly can have very distinct and different priorities to rural areas, and in the US that is one of the biggest factors in voting (tbf most countries do have at least
some urban vs rural split)
Self segregation. A city attracts a specific type of person, same with a suburb, a rural area, and all in between. Less because of political views but more because of community, schools, job, income, and culture. The result is that the largest areas are often just as unrepresentative of country as small areas.
This is not just the US. I struggle to think of any country where the cities are representative whatsoever. The closest is perhaps Stockholm in Sweden, but the other cities are not.
I mean, in Spain other than Barcelona (waaaay to the left of the nation) and to a much lesser extent Bilbao (nominally in-line with Spain at large, but with very different party makeups) for obvious reasons; the major cities voted fairly in-line with the nation. Then again, party differences in general here are smaller than the US (again with the Basque/Catalonia exceptions). Rural Castille votes at most around 65-35, not the 80-20 of the Great Plains for instance. (and interestingly, within rural Castille; it's not like the cities like Salamanca or Ávila are particularly more liberal than the villages)