It’s just impolite.
Most airplanes don’t allow their passengers to have much private space. That’s why it’s important to respect each other’s comfort and not spoil the experience of the trip. Even though airliners have no public policy that prohibits removing your shoes during a flight, the view of your naked feet can make other passengers feel disgusted and disrespected.
The flight can make it harder for you to put your shoes back on.
During the flight our body can change under the pressure it experiences. This means that our ears can pop, we can taste food differently, and our hands and feet might swell. So, if you remove your shoes before take-off, you might experience difficulties after you land.
It is extremely unhygienic.
Some passengers don’t even bother wearing their shoes when visiting the toilet. A plane’s restroom might seem nice and clean, but in reality you never know what previous visitors did in there before you entered. For the sake of hygienic reasons, it’s better to have your shoes on while visiting the restroom. Also, some flight attendants even confess that they feel annoyed when they see passengers entering this place barefoot.
It might create problems if there’s an emergency.
If any emergency happens, during the panic, any little thing can make it hard to evacuate. If a lot of people remove their shoes, they might end up scattered all over the ground. This debris not only gets in the way of other passengers making their way to safety, but also make it hard to move for those who removed them in the first place.
A possible solution
It can happen that you are just too tired after your travel and after hanging out in the airport for half a day. When you finally get on the plane, you might want to free your feet from your uncomfortable shoes and let them relax a bit. You can do this, but just keep your socks on. Though, as soon as you feel that they’ve relaxed a bit, it’s better to put your shoes back on.