If you are going to chage for shipping make it CLEAR in your Pledge Description in addition to the front page verbiage. Also mention it frequently and abundantly in your update emails about estimated delivery.
Better yet just factor it into the pledge levels and if you think the freebies from the stretch goals is going to blow your shipping budget then learn to factor that in as well.
Nothing more will sour a kickstarter then having to make a second payment to get the items you been patiently and generously, waiting for.
And I am not naming names as the company in question has done outstanding work in all other aspects.
Note that the shipping payment is NOT automatic. In my case it was an email requesting that I pay via PayPal. So if you have an issue you will have some time to respond rather than seeing money out of your account.