It should work just fine. The system-wide file that causes your per-user configuration lives in
/etc/fonts/conf.d/50-user.conf (actually it's a symlink to a file in
conf.avail, but it's its presence in
conf.d that makes it work here). Do you have that file?
If you're using 12.10, you'll see in it that the
~/.fonts.conf* locations are deprecated, meaning that support for them will be removed in a future version, so you shouldn't put your configuration there. Put it in
$XDG_CONFIG_HOME/fontconfig/fonts.conf instead. On Ubuntu by default
~/.config, so if you haven't changed this (which you probably haven't) the location for you to put your per-user customisation is
When using 12.04, however,
~/.fonts.conf is the right location as you'll see that
50-user.conf doesn't have the other entries there. You should try to remember to move your configuration to the new location if you upgrade to 12.10, but it should still keep working for this release at least.
Give it a go and let me know how you get on.