You will need the 'pcre' and 'gd' PHP modules in your command-line PHP. The command-line tool runs using the command-line PHP which is not always the same as the server-side one. In some situations it is possible to have two completely different PHP installations serving these two - if you install from a package, then re-install from source, but to a different directory, for example. The CLI tool should warn you if the part it needs is not present.
Before you start using it, you might want to change one PHP setting. Weathermap uses a fair bit of memory by PHP standards, as it builds the image for the map in memory before saving it. As a result, your PHP process may run out of memory. PHP has a 'safety valve' built-in, to stop runaway scripts from killing your server, which defaults to 8MB in most versions (this has changed in 5.2.x). This is controlled by the 'memory_limit =' line in php.ini. You may need to increase this to 32MB or even more if you have problems. These problems will typically show up as the process just dying with no warning or error message, as PHP kills the script.
Unpack the zip file into a directory somewhere. If you intend to just use the 'traditional' hand-written text configuration files, then it can be anywhere on the same server that runs your data-collection software (MRTG, Cricket, Cacti).
You'll need to edit two lines in the weathermap file:
from a shell or command prompt, and get a (rather boring) weathermap.png file in return. If you don't, you should get some kind of error to help you figure out why.