This is a known issue. The Extension Host sometimes fails to finish initializing on startup, which causes source control, terminal, and extensions to all fail to load. Our team is actively investigating it.
A workaround that has helped others is deleting the workspaceStorage folder – Cursor will regenerate it automatically. On macOS, the path is:
~/Library/Application Support/Cursor/User/workspaceStorage
You may also find this related thread helpful: Nothing initialises include source control providers, output, extensions etc