I think this mostly comes down to things like vendor lock-in. Yes, the tool enables you to more effectively do something, but at the cost of certain freedoms to you.

For instance, I can buy a hammer because it will make it much easier to drive nails than without one, but the handle is too long. So I can saw the end off to suit my purposes. You can't with proprietary software.

Also, don't make the mistake that free == libre. It's the fact that you're paying for proprietary software, not that your paying for it.