There are three ways to activate and deactivate fonts in Fontmatrix:
Selective way. In Browse Fonts sidebar go to Names tab and enable or disable particular font faces or even whole families.
Mass activation/deactivation via menu. Filter out fonts, e.g. by selecting a tag in Browse Fonts and use Edit > Activate all current or Edit > Deactivate all current to enable or disable all currently filtered fonts in the Browse Fonts sidebar.
Mass activation/deactivation via system tray. Use right mouse button click to open menu where you can click on names of tags to activate or deactivate fonts that have this tags assigned to them.