The best way to ship products like M:TG cards is to keep them very close and tightly together. Think of how tight the cards are when brand new and inside a booster foil. For sending 2nd hand cards to another person such as selling through eBay, same principle applies, use both thick cardboard and bubble wrap to protect and stop the cards moving whilst in transit. If shipping these cards together inside say a box designed to fit the cards, use clear sleeves were possible, this assists with stopping the cards from rubbing together and scratching one another, if you do not have enough cards to fill the box, look at adding bubble wrap to keep the cards tight.
Charging for shipping comes down to personal choice. Do you wear the cost of shipping as see this as a form of adding value to your customer base, or do you charge your customers for shipping as almost all customers know this is a valid form of a cost of doing business and realize you make a small profit form that as well.