I can think of a few fairly simple reasons.

As others have noted, there is the possibility of slipping on that nice granite flooring and sustaining a nasty bump - legal implications are ghastly.

Then there's the hygeine angle - suppose you get a verucca/fungal infection from a re-used pair of covers.

Making certain that covers are not oversize, torn or otherwise liable to be a trip hazard is a bit of extra grief.

Finally, flying is deemed by some environmentalists to be a massive polluter, what with the fuel burn etc. add on that it now means creating a mountain of plastic which probably won't be either recycleable or biodegradable and they will really get out of their prams...