99 Civic
this morning when I went out to go to work, there was frost on the inside of my front windshield. It got at or below 0F last night with even colder windchill factor here.
Is there a way to prevent this from happening again, besides replacing all the rubber seals?
I don’t think it has anythng to do with the rubber seals. Cold air holds less moisture than does warmer air. The humidity inside the car condensed on the windshield and then froze.
The only thing I know to prevent this from happening is to drive with the heater off and then take a tip from the dogs and drive with your head out the window so that your breath doesn’t fill the cabin with moisture. I’ve scraped the inside of my windshield countless times in bad weather.
run your heater and A/C …defrosts windshield faster…keep windows open to remove moisture from inside car…snow from shoes/books etc…it will go away over time.
I’ve been fighting this for years on my '06 Ford Escape hybrid ( since 9/3/05 ). Body shop found no signs of moisture intrusion and suggested it is retaining moisture better than my other two trucks which are driven and stored in the exact same conditions side by side. So far this season there is no frost on the inside ( knock on wood ). While pulling to my parking space I roll down a back window and blast the heater on high, There is moisture absorbant in many locations inside the car ( sticks of chalk, and silica jel packs ), And I cleaned the inside of the windshield with vinegar & water. I can’t prove that any one made a difference but so far , so good, and there’s snow on the ground right now.
I do have one packet of the silica gel, I believe it is, under my driver’s side seat. This morning was a little bit warmer and only a tiny bit of frost on the outside of the window, so I’m very thankful for that. That and the fact I don’t have to work the rest of the year now. 
Make sure you don’t have the cabin recirculate mode on, it should be venting in from the outside i.e. fresh air. Windchill doesn’t have anything to do with it that’s just a theoretical value.
I have 99 Civic, too. All the advice others have given is right on. I would add: make sure your heater/AC is set on fresh, not recirc. If there is a lot of moisture inside the car, beyond what can be got rid of by AC/def on [read your owners manual to understand this], windows slightly open when parked, etc., etc., you could put a small electric heater in the car at night and run it with the windows slightly open. Remove the floor pads and bring them inside to dry out.