Description of problem:
similar to request in bug 1075706.
yum-config-manager should update config file provided on the command line (when provided) rather than /etc/yum.conf:
# cp /etc/yum.conf /tmp/yum.conf
# yum-config-manager --setopt='debuglevel=9' --save -c /tmp/yum.conf
# grep debuglevel /etc/yum.conf
# grep debuglevel /tmp/yum.conf
yum-utils-1.1.31-28.fc21 has been pushed to the Fedora 21 stable repository. If problems still persist, please make note of it in this bug report.
Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.
For information on the advisory, and where to find the updated
files, follow the link below.
If the solution does not work for you, open a new bug report.