It depends on the nature of the frigate defenses. You obviously can’t depend on one type of cruiser defense to counter the myriad of possible frigate offenses.
Frigates are more defense dependent than cruisers are. The typical frigate weapon has 10 hitpoints - they do not last long once defenses are bypassed.
The standard frigate shield that everyone uses has a recharge rate of 7, which matches most cruiser shields. When I make a frigate team, I try to use every advantage I can to make incoming damage inconsistent - high speed, point defenses, multiple shields, distraction methods - in short, defense by statistic. If you can keep the incoming damage at a low incidence and spread across multiple craft, you can buy a lot of time for your frigates.
This makes some of the rapid fire cruiser weapons an unintuitively bad choice. While CL spam sometimes works just by powering through slower or larger frigates, the better tracking weapons like pulse lasers and quantum blasters take an embarrassing amount of time to actually bring down frigate shields due to recharge rates. Pulse can work if you heavily mass it and use it cooperatively; QB’s are just a total waste of real estate and cash.
The enemy of a high-recharge-low-capacity shield isn’t low sustained damage, it’s large damage spikes. This is why rocket fighters are so dangerous to frigates, not because they can merely penetrate shields, it’s because they do it in squad-wide volleys.
Focused high tracking, high delivered damage weapons are your best bet for shattering through frigate defenses.
Painted fast missiles ignore both size and speed bonuses of frigates; although you’d better be using painter fighters because the cruiser painter takes too long to reload. Heavy beams all hit hard, but the fed fusion beam in particular has an attractive 1.5 tracking and hits for 26-52.
If you want an example, SAC-20 is one of the most unpleasant fleets of the set to send close-range frigates after, despite having very little in the way of rocket fighters.
It seems there is an intentional hole in the cruiser armaments for fast frigates to exploit, however. The best answer isn’t always going to be another cruiser.