If you have to install a .cer certificate with an msi installation, then you have to be aware of a few things:

With Wise Package Studio (WPS) go to the MSI Script tab and choose 'Execute Deferred'.

You have to include the certmgr.exe (download from Microsoft) in your package.

The command looks like this:

certmgr.exe -c YourCertificate -s Root -add

Be sure to change on the Properties tab the In-Script Option to 'Deferred Execution - User Context' otherwise the certificate will be imported into the Administrator account and will not be available to the user.

Finally, in the InstallExecuteSequence table set your Custom Actions Condition to 'NOT REMOVE~="ALL"' to ensure that your Custom Action will not be executed during an uninstallation.

For more information regarding certmgr.exe click here.