They get paid by supplying services for the S/W, running adverts on their site doing professional installs and customisations for clients. Don't worry about them, they will still earn from it.
Linux, Apache (the webserver that most of the internet uses), ZenCart, osCommerce, MySQL etc, etc are all open source and have been for years. Yahoo and Sony use FreeBSD for their webservers which is open source, so just because it's free doesn't mean that it's not as good as some of the commercial versions, in fact often the opposite is true.

Once it's open source and in the wild they cannot charge for it later unless they change the licensing when they release a later version. Any version that is released as open source will always be open source.

__________________
Lawrence