Customising Communication Sites?

I don't believe that you can change the font used at this point. In the official documentation on customizing modern team sites (which basically goes to communication sites as well) their example of applying a custom theme (using PowerShell) uses a null-value for the font-scheme URL - so I suspect that it cannot be done (https://msdn.microsoft.com/en-us/pnp_articles/modern-experience-customizations-customize-sites#applying-custom-theme-to-modern-team-site).

Furthermore these modern sites uses a lot from Office UI Fabric (https://dev.office.com/fabric#/styles/typography) as it's the official Office Design Language. The default font is "Segoe UI", which also is used on modern sites. They also use the base classes for sizing (ms-font-m for example), which is a part of Office UI Fabric.