Why is VAT charged on shipping?

In Europe taxes and duties are levied on all “incidental expenses”, including transport and insurance charged from the end-customer.

Article 78 of the VAT regulation:
The taxable amount shall include the following factors:
taxes, duties, levies and charges, excluding the VAT itself;
(b) incidental expenses, such as commission, packing, transport and insurance costs, charged by the supplier to the customer.

The applicable tax rate is based on the tax rate levied on sold goods.