Because fundamentally, if a craft is safe to send humans to orbit you want to send humans - not cargo, which is cheaper to send with a craft which is less safe.

You are correct to say that using a human-rated system to launch cargo is usually much more expensive than necessary, as was true of the space shuttle. This does not mean that the cargo causes any safety problems.

Indirectly, as you have to launch another spacecraft for the same number of people to get to orbit.