I recently saw Underworld: Awakening.
One of the main premises of that movie was that the Big Secret got out and Humanity went nuts. The first few minutes of that film describe a Purge that make the witch hunts look mild - teams going house to house, testing everyone for signs of "infection" with any resistance being met with enough firepower to put down a supernatural. Informant lines set up so you can report anyone you suspect of being supernatural, specials guns and ammo being developed, squads armed with flamethrowers - and everyone on a team in constant communication so any contact brings backup in minutes. Add in the helicopter gunships, tanks, rocket launchers - combine with overwhelming numbers - and the supernatural types didn't stand a chance.
That's the sort of thing that the Supernatural types in the DV worry about. They have power, but humanity has numbers, tech, and ingenuity.
When it comes to "the government knows" type things, I think it's a bit like the old Word of Darkness where there were small groups that know - and since they don't want to cause a panic they keep things to themselves. "Project Twilight" was a small FBI division that handled all of the X Files type cases and knew a bit about Vampires, werewolves, etc - enough to show up and toast anything that made itself a bit too public. I can see a small unit like that existing in the DV - sending teams to deal with things that get out of hand. Maybe even tying in a bit to the Paranet as infiltrators.
The RPG suggests that most towns have a SI branch of their police department or someone/something that does the same thing - keeping the lid on the supernatural and dealing with things that get out of hand. Maybe it's not a cop, maybe it's the local supernatural boss who doesn't want anyone to make waves, but someone does the job.
And that's the only way supernatural beings can work in a small town. If someone is killed there's a big outcry to find the killer. If someone's house gets torn up, people go missing, telephone polls get tossed around, or anything else that would be noticed, then it doesn't matter that no one on three man police force can even spell forensics - they have the phone number for the state police, FBI, homeland security, and every other law enforcement agency out there. Leave too many clues and the investigation will get closer and closer to revealing the supernatural world - which encourages supernatural types to find scapegoats.
If battles start becoming too public, I can see virtually anyone in a position of authority sending the PCs a message to "keep it down". The local Red Court Noble, a Winter Court Fae, any White Council Wizard - if there's an NPC with standing then I can see him sending the PCs a reminder saying "if this goes too public we all lose". And if any of the PCs belong to Accord nations I can see someone from another nation calling their nation and saying "looks like you have to do some housecleaning here".
Then again, that's the default setting. If your group likes playing in a world where the chief of police has the local heads the Red Court, Winter Court, etc on speed dial, all the reporters know why some articles never make the paper, and its only the great unwash that are in the dark then that's close enough that most of the DFRPG can work in that setting.
Richard