I think that's kind of the point, any two city pairs don't actually have the full capacity of a high capacity line.
It's much better to look up the actual capacity of stations. If you take something like Liverpool Lime street usage is more like 3000 people per hour. That's more like 150 flights and hour or 1 per 24 seconds. Which is easily doable with 10 pads if the vehicle taxis away after landing. Thus the actual land area for something with the capacity of a mainline station will fit within about the same area as a mainline station.
In practice I would imagine that you'd utilise existing roof space from multistorey car parks near to station or bus stations first. It also has the advantage of scalability, you can build for initial demand and add more pads and charging spots as you go.
I also suspect that eVTOL will probably mostly be used to make trips that you can't today, particularly leisure trips. Today if you wanted to visit a North Wales beach from Manchester on a Friday night when there's good weather with no planning you couldn't do that easily. With eVTOL you could be there a hour after you left work with no need to build high capacity infrastructure to do so.
Air space is not really an issue for capacity there is a hell of a lot of it and automated ATC, sense and avoid systems and "air routes" are all doable. Relatively easily from a technology perspective, the issues are planning and chucking GA aircraft out of a lot of the airspace. I think a lot of those issues will be resolved once people start flying on eVTOLs and how useful they could be to them/FOMO from watching people in other countries.
I think all of this will pretty inevitably happen, timing will be the issue, but in the long game high capacity batteries and ever increasing computational power pretty much guarantee that this will happen.
So in addition to 10 pads you need somewhere for the aircraft to taxi to, assuming that there's going to be some margin of error it's not unreasonable that 10 pads is going to be at least 200m long and 20m wide you then need extra parking spaces.
If we assume that those pads each need say 5 spaces linked to it (note the 24 second assumes that every 20 seater aircraft is 100% occupied - whilst the same could be said about my railway line, trains can have people standing, 12tph can be increased, 15 hours per day is 6am to 9pm, so there's still a bit of extra capacity), that would allow each space to be occupied for 20 minutes.
In that time those aircraft would have to land, taxi to their space, be emptied, be cleaned and reloaded and be back in the air ready for the next aircraft to land. Likewise each pad would need to land and taxi off one aircraft and then taxi on and clear the landing area every 4 minutes. Whilst Heathrow manages it much closer times than that, they are always moving along, which isn't something that a vertical take off aircraft is doing (as it's likely to be coming downwards a lot more than traditional aircraft.
As to air space, it's likely to get very busy very quickly (not the 100km upwards - as that's not really a limiting factor) as a lot of people would want to be landing in some fairly dense places.
Whilst Liverpool Lime Street may be 3,000 per hour (pre COVID that was the average over the whole day, so peaks would have been noticeable busier than that) Manchester Piccadilly is about double that.and that's only the 10th busiest station in the UK.
For there you're at a flight every 12 seconds (again peak demand is likely to reduce that further).
That's also not allowing for the potential for future increases in rail use (HS2 trains, if the full station was every built, could provide capacity between Manchester and London of 3,300 seats in each direction compared with the current circa 1,800 seats in each direction).
The per person land requirement for each rail passenger (based on Network Rail land ownership) is 0.331m2, this compares with 0.201m2 for Heathrow. Whist that sounds an easy win for aircraft in terms of aircraft, it's comparing the busiest airport with the whole of the rail network (which includes a lot of very lightly used lines and stations), it also only compares one end of the route, so at the very least we need another Heathrow for people to be going to, which puts air travel at 0.402m2 per person.