That's how angular works.
If you use AngularJS, you'll pretty soon see a cleaner separation of concerns in your code than you've seen in other styles of web development. Sure, there are references to JS functions in your HTML. But you can easily move around HTML without worrying about breaking code, and your JS is clean, testable, and does not rely on a very specific DOM. This allows you to reuse business logic better AND reuse HTML better.
Bottom line: don't stress about it. You'll get used to it quickly enough. And don't resist things just because you were always told that the other way is The Right Way.
If you feel it's important for your HTML to be compatible with the standard, you can use the
data- prefix on your angular directives: ie,
data-ng-repeat= and your HTML will be W3C compliant. Personally I never worry about it, but doing it is harmless.