That's why I never charge your credit card until I am ready to ship your package. If the shipping amount is too high, I will adjust it and charge you the correct amount. If you actually make the payment through paypal or by check before I have a chance to edit the shipping, I will refund any shipping overpayment.
Also, I never add a "handling charge." I prefer to ship priority mail (the price is usually comparable to parcel post, and sometimes even less!) unless to ship to your zip code is more economical by parcel post -- then I will ship whichever way gives you the most reasonable shipping fee.
I use free priority mailing boxes, or recycle boxes whenever possible. Occasionally I have to purchase boxes in order to have the correct size, and that will add a small amount to your shipping costs.
The bottom line -- you will never pay more for shipping than what it cost me to ship it to you!