The Per Unit perweightunit is based on the products_weight x quantity in the cart x Per Unit Rate ...

If you set in the Modules ... Shipping ... Per Unit perunitrate to 1.00 then when you set the Product Weight to:
Add Qty 1 x 0 (product_weight) x 1.00 (Per Unit Rate) = $0.00 shipping
Add Qty 1 x 2.50 (product_weight) x 1.00 (Per Unit Rate) = $2.50 shipping
Add Qty 1 x 3.00 (product_weight) x 1.00 (Per Unit Rate) = $3.00 shipping
Add Qty 2 x 2.50 (product_weight) x 1.00 (Per Unit Rate) = $5.00 shipping
Add Qty 2 x 3.00 (product_weight) x 1.00 (Per Unit Rate) = $6.00 shipping
etc. etc. etc.

So the Shipping Cost will be calculated based on individual Product Weight ...

So, for the Products set to 0 weight, you are saying you want "free shipping" as 0 x any quantity or rate will be 0.00 ...