The "regular" guns on the cruisers can still target fighters.
TBP has been changed so that the most powerful guns on capships will only shoot at capships now. This means the big turrets wont waste their firepower trying to swat impossible targets like Starfuries and will instead do what they're supposed to do: pound other capships!
This also puts a bigger emphasis on fighter cover. Ships like the Nova, for instance, only have a small handful of guns capable of hitting fighters. While these guns are good at what they do, mass fighter attacks wield the potential to inflict grevious damage on a Nova if it's not protected by its own fighters.
Trust me, it's fun.