Well, in my computer those files are symbolic links, not folders... check if in your case they are folders, and if so, close Steam and "rmdir" those folders to see if Steam stops giving you this error.
These messages are due to folder layout changes in Debian's steam package (compared to Valve's .deb package), which got inherited by Ubuntu, and Linux Mint. As such this will need to be addressed by a package maintainer for Steam in one of these distros.
It should be noted that that this issue is harmless in practice.
Nothing extracted yet.
I have new mint 17 install.
from console
steam
rm: cannot remove ‘/home/j/.steam/steam’: Is a directory
rm: cannot remove ‘/home/j/.steam/bin’: Is a directory
Running Steam on linuxmint 17 64-bit
STEAM_RUNTIME is enabled automatically
Why it wants to delete those directories?
I have had new install of mint17 and steam and I have at least 2 times now noticed that my downloads have started from begin. I think both times I had just closed min17 from menu --> restart or shut down. And I quess steam doesnt close cleanly.