Where you depart from in major cities then yes you will fly over major cities. However, as a rule of thumb you won't necessarily be flying over cities, or alteast in the built up areas.
For example, a London helicopter ride will depart from Battersea, so you'll be flying over London but not the city centre - which tends to be the area passengers want to see most.
Instead you'll still see all the sights but from a far.
If taking a helicopter ride in New York, then that's different. Skyscrapers will obstruct major streets and tourist attractions, so would be limited somewhat, as you'll stick to flying over the river as oppose to the densely populated city.