I’m giving you the same answers as Apple not because I work for them (if I do they’ve been forgetting to send me a paycheck for decades now), but as Apple decides whether they’re going to replace your phone, and they have been clear about the fact that this is not a defect, why wouldn’t I tell you the same?
Scratches do not come from denim pocket materials, they come from small particles of sand or other hard material that actually collect in pockets as a matter of course.
You could rub the screen all day with a soft denim cloth and not cause any scratches; the softest microfiber cloth with a few small grains of sand embedded likely would.
To not use a screen protector is akin to never washing or waxing your car; you don’t have to but your automaker won’t cover it when the paint fails either.
To use your example, the wind often does have sand and other particles in it, and if your paint is scratched for any environmental reason or your windshield chips, it won’t be covered. Feel free to call any auto dealer to verify.
As far as Tom’s, like many such websites they make their money on traffic, and nothing drives web traffic like a good “Apple has a defective product” story. Tom’s also knows well that all other premium smart phones have people complaining about similar scratch susceptibility, as explained by the Verge article people love to dismiss.