The first step I'd recommend when securing a cPanel server is install CSF. CSF is a wonderful package which not only helps secure your server, but also has a full GUI interface on cPanel installs (you can find it in WHM, at the bottom of the left hand frame).

Installing CSF is incredibly simple (below commands taken from install.txt:

rm -fv csf.tgz
wget http://www.configserver.com/free/csf.tgz
tar -xzf csf.tgz
cd csf
sh install.sh

If you login to WHM, on the bottom of the left-hand frame will be a section for plugins, under which the CSF plugin sits. Open up this page and there will be a list of possible options.

Firstly start by changing the firewall from 'testing' to active (can be done in configuration).

Then, you should read through the server check list, which provides useful security tips of all aspects within the server. Note that you needn't implement every single suggestion, there are some which are suitable for certain environments (at the bottom of the results page you can re-run with all comments - this is probably the best way to do it).