How do you protect your cables on the floor?

Well, the system is next to an entrance and it is quite often to have people walking in between the amp and one of the speakers.

How do you protect the cables? do you cover it with the cable covers (large rubber mat), or cover it with carpets? Is there any creative solution with min. negative effect to the sound?

I simply can't stop my wife from entering the room from the entrance :-)
I have a similar situation, with a patio door between my equipment rack and speaker. My speaker cable tucks under the edge of the threshold. If you have a wooden threshold, you could always add a small trim strip to cover the speaker cable.
In our previous home we had this problem. We covered the speaker cable cable with a wool oriental runner.
You could use a cord cover like you would find at an office supply.
See my response under thread titled:

"speaker cable length does it really matter"?
If you have timber floors, and access under your house, I'd drill two small holes in the floor and run the cable under the floor.
You can easily fill the holes later when you no longer need them.