In the version of Safari that comes with OS X 10.11 El Capitan, Apple changed the behavior of the Command-1 through Command-9 keys. Before El Capitan, pressing Command-1 would open the first bookmark on your Favorites bar. After El Capitan, however, Command-1 switches to the first tab, Command-2 opens the second tab, and so on. If that’s not how you want to work, choose Safari > Preferences > Tabs and deselect “Use ⌘-1 through ⌘-9 to switch tabs.” From then on, Command-1 through Command-9 will once again open bookmarks. Regardless of which behavior you prefer, you can reverse it on any invocation with the Option key, so if you set Command-1 to open your first bookmark, Command-Option-1 switches to the first tab.
