Have you found a cure for this yet?
Actually, I found a workaround. Looks like there is a syntax problem with the tcl script, it appears to try to clear the -readonly permissions on the various files. My knowledge of tcl would fit on the head of a pin, but according to the tcl documentation I found you can only do that on a Mac. Linux allows you to do -owner and -group and -permissions, which makes sense for linux filesystems, I guess. Anyhow, hence the error.
This -readonly thing is done in several places, but the one that causes the problem you describe is in the "qsim:open_project" procedure. If you edit the file quartus/common/tcl/apps/qsim/qsim_script.tcl and go down to line 1413 or so you should find:
file attributes db -readonly 0
comment this out by putting a# in front and save it and you're good to go. If you feel keen, you could find the other places the file attributes -readonly function is called and comment them out, too. If you were feeling super keen, you could fix the tcl to use something cross-platform compatible and submit a patch to Altera.....
Hope this helps.
A/B