It would seem like nails lying flat would stay flat when run over by the tire and most likely wouldn’t puncture it. If the nail were lying flat and it had an average size nail head, the nail might start to move vertical when the tire rolled over the nail head but wouldn’t the weight of the tire on the sharper end keep the nail from rotating into the tire? I can see that a nail sitting vertical on it’s head might puncture it but that would seem less often the case. Seems like the frequency of nail punctures (I don’t know what it is), is higher than it should be.
The nails in tires are rarely straight. Other cars fling them up and the car behind bends the tip, them spits them out again.
A nail lying on it’s side will have the head bent ninety degrees when a car runs it over. Now it looks like an upside down check mark, which, in just the right circumstances, can turn so that the point is sticking up.
A nail gets caught between the treads of your tire. As the tire rotates, the nail drops off just in front of the tire and bounces on the pavement. Then is rolled over in mid-bounce.
If you are prone to picking up nails in your tires, you’re driving too close to the inside shoulder when going around off-ramps. It’s neither the fastest nor the safest way to go through a turn and you should stop doing that. Off-ramps are the usual culprit because they usually curve upward rather than down, and stuff rolls down and back from contractor’s trucks. The inside shoulder is more often the culprit because of the camber of the roadway. If the inside shoulder was higher than the outside, everyone would slide off the turn.
Man you nailed it!
What if the nail were originally in a thin piece of wood so it stuck up, then after getting stuck in a tire the wood got worn away?
Nails may lie flat on the pavement when they come to rest, but they get kicked up when run over. If a vehicle in front of you kicks it up and it’s still tumbling when you reach it, you may end up running over it in an orientation that enables it to puncture your tire.
Even if no other vehicles are on the road, your front tire can kick up a nail, resulting in a puncture for your rear tire.
Based on…what? An arbitary notion of how often tires should be going flat?
If you ask anyone who has had a number of flats, you will confirm that a far greater portion of them happen to the rear tires. This is true of cars, motorcycles, & bicycles IME. The explanation that makes the most sense to me is that the nail is lying flat, just as the OP suggests, when the front tire goes over it. But the front tire then lifts/spins/kicks it a bit, and then it might be in a position to puncture the rear tire which arrives a fraction of a second later.
Or think of it this way - many nails are driven over and don’t wind up in the tire. It may be a rare occurance, but it does happen occasionally to some people some times, in the manners suggested above. We don’t ever notice the nails we’ve driven over and that didn’t stick into the tire. But think of all the nails that must be on roads.
I laughed.
Got nails in your tires? Screws? I did. Close observation revealed two kids placing nails in my tires so when my car rolled the nails/screws would puncture the tires. Check out your neighbors if you are getting flat tires all the time. Or your workplace. And by the way, when the two kids moved away I never got another flat tire.
If you don’t know what it is, then how could it seem higher than it should be?
This is what we call confirmation bias.
OP’s question: How do nails end up in tires?
The Devil puts them there!
Way back in the day a girlfriend of mine called me to come over to her house because she had a flat tire. It was the left rear tire. I had to move the car a little bit to find the hole, but when I did I found a wrench head almost completely flush with the tread.
She had run over the wrench with the front tire, which caused it to pop up enough to puncture the rear tire and push 95% of the wrench through the tire.
So - nails. Pshaw. Until you are stuffing tools through your tires, don’t talk to me. 
Last year I had a dinner FORK puncture my tire! Only the handle was sticking out. And it was hard to pull out since 2 of the 4 tines were bent at 45 degree angles, inside my tire. That was my only flat tire in 20 years of driving. A nail I could understand, but a forking fork? What the fork?
Just got a nail today and I was going to post this question. My father claimed he got 4 in 1 day by running over a bunch of nails. Maybe it was just a tall tale.
Nails? how mundane. Check out those buckets on the counter at many tire stores. I have seen screwdrivers, wrenches, metal brackets, bolts and more. It is amazing what gets into tires.
I know this is a zombie, but I have to ask a related question. How do nails get into the sidewall of tires? I’ve only once had a nail in a car tire (don’t ask about bicycle tires) and it was in the sidewall. How in hell could that happen (other than some malign being intentionally inserting them)?
Hah! I once had a tire patched in college, and while I was waiting, I was looking at the clear plastic jar of crap they’d pulled out of tires over time. It was mostly the usual assortment of wheel weights, nails, screws and random assorted pieces of crap.
But what caught my eye was the nearly 3 place-settings of flatware. Apparently one day after the end of the semester someone’s box with their silverware had flown out of their pickup or whatever without them knowing, and the tire shop had pulled nearly 3 full sets of silverware out of other people’s tires over the next couple of days.
Never expected to see spoons, knives and forks in that jar, that’s for sure.
One time several years ago, I was driving down an alley. I swerved to avoid running over a board (after all, sometimes boards have nails).
One of my tires picked up a nail that I would have avoided if I had gone straight.
I’ve recently taken up walking / jogging outdoors. There are a lot more rusty nails laying around than you might think. My usual distance is about 3 miles or so, and I take different routes each time. Even over a mere three miles, I see a good 10 or so rusty nails laying around (on the sidewalk) every time I go walking.
Ahh, the proverbial fork in the road!