My problem was caused by an insecure configuration of the sudo system. When I installed my Arch Linux system and to have the hability to execute commands without the root account, I added directly my username in the sudoers file like this :
martin ALL=(ALL) ALL
It worked very well with sudo but not at all with polkit. With this configuration, when I just typed `pkexec` in my shell, it opened a root shell without asking me for any password. But when Nautilus tries to access the `/root` directory, he execute the `pkexec` command. So that I could go in this directory without any password with my normal user account.
To correct the problem, I put my user in the `wheel` group and uncomment this line in the sudoers file
# %wheel ALL=(ALL) ALL
In conclusion, it's not a security breech in Nautilus but an insecure configuration I made...I'm sorry.