There have been changes in the file system on Yosemite that may affect also the position of the core fonts shipped within XQuartz.
Please confirm that on your Mac the directory /opt/X11 exists while /usr/X11 is missing. In such a case, you can create a symbolic link to work around the issue by executing the following command in a Terminal:
sudo ln -s /opt/X11 /usr/X11
We’re going to open a Trouble Report and release a fix soon.