eBay often run multiple promos concurrently, and now sellers can send out store-specific codes too. You either have to tick a box, or enter the code manually, because you can only apply one (actually not sure if it will let you apply an ebay and a seller code at the same time, but you can definitely only use one eBay code), so having a discount apply automatically means you can't choose which is the best voucher to use. Not to mention it would mean it'd apply on any eligible transaction and then we'd get lots more "I didn't want to use it on that particular transaction" threads posted here.
That's the same reason a lot of sites don't do automatic discounts, or if they do, it's only every now and then - I currently have an automatic discount set up on my site, but it means if it applies to an order, they in fact can't use any voucher code at all. This can be a problem if I've given someone a unique discount code for some reason that's a better discount than the auto one.
Also, the way ebay's discounts work, there would be no way they could provide a "forgot to use a voucher" system of compensation. When an eBay code gives you $X off a purchase, the purchase price itself is not actually discounted, the seller gets the full, original asking price as a payment, it's just co-funded by eBay, so what are they supposed to do? Just pay you $X instead? Give you an extra voucher for forgetting? (I guess a lot more people would become very forgetful if they started doing either of those, lol, nice way to rack up some additional discounts).
