When you call new Vue(), you're creating what is called a vue instance. A Vue instance basically is a JavaScript object that has some capabilities to interact with the DOM.
Vue components happen to be Vue instances, too. But the main difference is that components belong to other components/vue instances, while bare instances are mounted directly into an existing element of the DOM (with existing, I mean HTML that is not generated by Vue and existed previously to the instance creation).
So, basically, the main difference comes from the use: you usually create a bare Vue instance with new Vue when you need to attach that instance directly to the DOM as your root element. Vue components, on the other hand, are always attached to ** other components**.
In general, it is really common to have a single root vue instance in your Vue application, but you could have several bare instances in the same web page: you could get creative and span several Vue instances and make them interact with the DOM at the same time, as if they were components.
However, it is better to have a single root element with several components, since it is easier to reason about your code in that way, and also facilitates the use of plugins like Vuex or Vue-router.
Maybe this link about this matter can serve you as well.