WebMatrix currently offers 3 methods for publishing: Web Deploy, FTP, and FTPS. What’s different and how can you decide between them?
For starters, your choice of hosting provider may be a factor – not all publishing options will be available from all hosting providers. The hosting providers shown in the Publish > Find Web Hosting in WebMatrix do support all 3 types of publishing, however outside of these providers, you are not guarenteed that FTPS will be enabled or that Web Deploy will be on the hosting server. My personal publishing preference is the Web Deploy method because it does a selection of steps for you automatically during publish so you don’t have to do them separately – which just makes publishing easier (and it's also faster than FTP).
Here’s a tabular comparison of the options to get an overview of some of the ways these publishing methods differ:
And thanks to Ben Byrd for his FTP insights and helping to make sure this table is accurate!