You pay the exact amount for things if the purchase process would end up requiring you add $5+ to your wallet.
By adding money to your wallet on your own, you screwed yourself.
Go through the process procedure without money in your wallet and it'll end up prompting you to charge the exact amount.
Judging from your posts, the reason this didn't happen is because you'd already charged $5 to your wallet. This means you need to charge a few cents to cover taxes. Since you can only charge a minimum of $5, you have to charge $5 to cover those cents.
If you'd had nothing in your wallet, you would've been prompted to charge the exact amount instead.
Edit: A probable reason for the minimum fund limit is credit card transaction fees. Every time they make a transaction, they have to pay a fee and if the charge is too small that fee can be too large a percentage of the cut to be worth it. Because of this, many companies will enforce a minimum charge.