In my understanding, "Y" is something of a subclass - usually indicating a higher trim level of a particular vehicle or a vehicle that is in limited supply (ie Honda, Subaru).

For instance, a base model Ford Fusion would be classed "F" but a Fusion Titanium would be classed as "YF". Likewise a Honda Civic or Subaru Impreza would usually be classified as "YC" since they're rare and therefore more highly desirable C class vehicles.

The "Y" is how Hertz could claim you're getting a free upgrade(!) even though they're just tossing you a higher trim level in the same class.