Target (and Home Depot, etc) were hacked because when a card was wiped on the PIN pad, the PIN pad sent the card number over to the cash register in clear text (not encrypted). Malware on the cash register was able to scrape the card numbers out of the cash registers memory, save them, and ship them off to the hackers.
With point-to-point encryption, when you swipe your card (or insert a chip card), the PIN pad itself encrypts the card data (in a tamper resistant part of the PIN pad) with an encryption key that is unique for that specific PIN pad. The encrypted card data is sent to the register. If there were malware on the register, it wouldn't see your actual card data, because it's encrypted. And since each PIN pad uses a different encryption key, even if hackers stole a crap-ton of encrypted transactions, they're going to have to crack each key individually. That's the one end. The cash register sends the encrypted transaction out of the store for authorization, and at some point (usually at the retailer's payment processor, or some other place outside of the retailers network), the transaction gets decrypted there, and then sent off to the issuer for authorization. That's the other end.
Any card used at Target or Home Depot is protected in that manner.