I'm also new to Shopify/Printful and have never posted in the forums before - but I figured this out today so thought I should share.
I ticked the 'display my product with free shipping' checkbox in Printful when I added products to my store. Then found that all my products have free shipping despite setting up shipping rates.
Here how to undo this:
In your Shopify admin: admin/settings/shipping
The second box should be your 'App shipping profiles'. Click on 'show' to reveal all the profiles. Then scroll right to the bottom of this list, clicking on 'show more' if needed.
This should be at the bottom:
Then just click 'manage rates' and deselect all the products that this rate is applied to.
Maybe you can also delete the profile, i'm not sure.
This worked for me, I thought I was going to have to add all my products again!