Look at the _Layout.cshtml. You will notice HTML5 tags such as <header> and <section>. It also includes the modernizr javascript plugin to the project.
When would you definitely not want to use it, only to keep compatibility with old browsers?
If you don’t want to use HTML5 specific tags. Anyway, it’s just a checkbox generating a bunch of default markup that you could modify at any moment if you will. So you are not engaging yourself with anything that cannot be undone subsequently. If you are starting a new project, go ahead and check it 🙂