It doesn't though. The vast majority of flights are short-haul or long-haul flights and not domestic. This data uses the UK flight data so let's look that up.
Non-Domestic flight passengers: 14,124,617 [1] Domestic flight passengers: 1,455,330 [2]
So you can see that over 90% of all passengers do not fly domestically within the UK. So only the domestic flights emit more CO2 than combustion engine cars, but they are the minority. If you were to look at the US, flights that short probably play even less of a role due to longer distances between cities in the US (in comparison to the UK).
In conclusion the data you provided very much proves my point so thank you for providing the source for my statement yourself.
[1] https://www.caa.co.uk/Documents/Download/10276/b2eedadb-6813... [2] https://www.caa.co.uk/Documents/Download/10276/b2eedadb-6813...