Because you're not discarding a card. Discarding a card is a separate mechanic (you can force your opponent to discard a card) and discarded cards go to your cooldown pile.

Ragpicker, Bonfire, etc. are [destroying[/b] a card. A destroyed card is removed from the game - regardless of whether it was in your hand, your play area, your cooldown pile or your deck, it can no longer be found. It won't appear in the tavern deck again after reshuffling. It's called "Destroy" and not "Gently reposition" for a reason. Think of it as you're taking the card and shredding it into tiny pieces right there and then - can't really say that the card's still in play and counts towards the combos because there's nothing left of the card but shreds. You do, however, keep all the previously acquired bonuses from it because the card was played and you got (and probably used up) the resources it provided.