The main reason is almost certainly to protect the product until it gets to the consumer. Letting the minis jumble around together during (especially during shipping) WILL damage the paintjobs. Additionally, it provides some padding against being crushed.
Well quite frankly they don't offer anything I have seen unless they are made to be instantly deflated and refill with air via some maigc because I have never come across one that will actually hold air but gentle pressure will make the bag deflate quite quickly.
I can se protecting paint rubbing, but it really doesn't offer any protection in the sense of padding beyond preventing paint form rubbing against each other. There is no impact protection.
I'm not sure I understand what you're suggesting as an alternative here? The cards can't be flimsy, so they print them on cardstock.
Unless you're suggesting they get rid of the cards altogether, which I'm not totally opposed to; I never use the cards, personally. (I never really played DDM, mind you.)
The cards could be flimsy-er, and don't have to be on premium gloss photo paper like the plastic coated poker cards. The point is many people under DDM would use a marker on a card inside a card sleeve so the card was protected. Lower quality paper would reduce costs. Since they no longer make DDM and DDM even allows proxy cards bia computer printouts, then there really is no problem there.
For the new minis you are right. They don't need the cards. They could sell a single pack of cards with the entire set in them and you have one for quick reference. You don't need to package a card with each mini since you don't need to use them like with DDM anymore to turn them or something to denote the figure has finished their turn. Also you can just use a token like many already do that could be a bonus to a complete card set that gives status effects and shows when actions have been used up or bloodied status exists.
There really does need to be no cards with the new product model. When you have the card for one Orc Brute, you have a card for all of them.
Minis aren't necessary, even for those games which are highly tactically-oriented, like 4E for example. In place of minis, counters are popular because of how customizeable and inexpensive they are, and token objects (candy, lego pieces, pebbles, or whatever) serve the purpose equally well, although they aren't as pretty.
You're right though, minis will always be back, as long as people are playing tactical RPGs and wargames. And in the meantime, people will use other objects and the minis that they've already got to represent their characters and monsters.
Minis are necessary for those of use that have collected them for years even before we played D&D.
I think a severe rethinking of the cards is in order and what part they will really play in the new minis product models. May be too late now, but selling the cards like the packs of Power Cards, would be better than trying to include a card with each mini. Then people who don't even use minis could make use of the quick monster cards and are more likely to buy them than having to buy minis to get the cards, and those who use minis and may not have the right minis and need to use a substitute until they pull the right mini from the random distributed monsters will at least have the cards upfront and can play until they pull the mini they need.
Probably these things are already in production and packaged and it is too late to bring this up, but I think adding the cards to a pack set and leave them out of the box could reduce costs if only a dollar per "booster" of minis, and also get other people to just buy the cards.

The cards will have the same rarity of the dang minis the way they are going to package them with the minis!