What I'd like to enable here is a progression where you start out prototyping your app with a single D1 database, which is easy to use and reasonably fast. Then as you grow we provide tools to let you transition to many D1 databases sharded in a way that makes sense (e.g. per-user). Apps that want even more control can move to using full-on Durable Objects (which will soon support a SQLite database per-object).
That said, there are certainly many use cases out there where simple monoliths make sense, especially non-interactive data crunching. I'm not sure yet if D1 will ever be the right choice for those, but the Workers platform aims to provide many options.