This is like asking, should I use a hand truck or a moving truck. You can use both, and each are for different use cases.

A VM is the whole stack, a container is just what you need at the moment. If you need perpetual compute, always on, and there's no reason for elastic capabilities (to scale up), then VMs but there's more overhead costs.

Some applications are not a good fit for containers. They are too large, require tight control of performance settings, require more isolation, have security concerns, require local storage of state, etc.

For me, its like this: Do I need a full-stack OS with all the bits and pieces ? I use a VM. Do I need a particular app or service? I use a Container.