You need to book using your Hertz Gold Rewards account. On your Gold profile there are fields where you can specify whether you want to earn Hertz points or frequent flyer points. It's in the membership details section of your profile:
And here is what it looks like when you click through:
Note:
Remember you can only earn one Reward Currency on any given rental so please chose either Hertz Gold Plus Rewards or a Frequent Traveler program for your rewards.
Hope this helps!