Last night I made a Hertz reservation at their website and there was no field for entering my flight number. There was the usual drop down list for choosing the airline. Once the reservation was confirmed I received a message from Hertz reminding me that it was in my interest to include my flight number in the reservation.
I sent Hertz an email (contact us) and described the problem.
I just received another email from Hertz and they acknowledged the problem and said it was temporary.
If you can't enter your flight number at the Hertz website this may be the reason.