Yes, your cause will get the full percentage of the purchase price (purchase price does not include tax, shipping, or handling). Stores that are listed with a "Special Rate" donation typically offer a flat-dollar rather than a percentage donation.
Some merchants may offer different donations for different products. Occasionally, some specific products will not be eligible for a donation. These donation rules/exceptions will always be listed under the "Exceptions" link in the iGive Mall, and in the Coupon Window which appears on the lower-right corner of your desktop when you shop.