Safety: Flying cars would reduce traffic density. If the cars can operate at, say, 100 different levels, then you have only 1% as much traffic at each level. Thus there is less chance that a moment of inattention will result in an accident.
On the other hand, you can now be hit by things coming from above or below as well as in 2D. It's more difficult for a human operator to manage.
On a road, if you see that you're in danger of collision, you may or may not be able to veer left or right to avoid it. There may be traffic in those lanes too, or obstructions on the side of the road. For flying cars, there might be other traffic, but there's not likely to be obstructions. And you avoid the collission by going up or down instead of left or right.
Airplanes today have a variety of collission avoidance systems. It seems likely that flying cars would, too. At the very least, something that would sound an alarm if you or another flying car are on a collission course.
Yes, when two flying cars collide they could fall on a bystander below. But when two cars today collide they might hit a bystander. As flying cars wouldn't be limited to roads, I'd think they'd be less likely to hit pedestrians. The probability that you will hit someone if you drop a rock from a random point in the sky over North America is way less than the probability that you will hit someone if you throw a rock from a random point on a paved road in North America.
Crime: Yes, I suppose it's true that criminals could use flying cars to circumvent things like fences, thus making security more difficult. I doubt this would be a serious obstacle to their development and use, though. Lots of inventions can be used for sinister purposes. We look for ways to protect ourselves, but we rarely abandon a technology because of this.
Like, talking over cell phones rather than face to face creates the possibility that someone could monitor the radio waves and eavesdrop on your conversation. How many people refuse to use cell phones because of this possibility? How many say that cell phones should be illegal because of this possibility? Or, someone could use a big heavy coat to hide a weapon. Does anyone seriously suggest that heavy coats should be illegal, and we should all have to freeze in the winter, because some use heavy coats to hide weapons? One could come up with thousands of such examples.
I presume that if flying cars became technologically practical, yes, criminals would use them to their advantage, and law-abiding people would look for ways to protect themselves. If flying cars were common, then a fence or even a stone wall would be almost useless for keeping people out. People who wever extremely security conscious might build domes over their property. People might rely on alarms that use radar or some such technology to detect when someone crosses the perimeter and sound an alarm. There might be higher-tech solutions, like force fields.
I think the real barrier to flying cars is cost. The technology has existed for decades to build helicopters. So why aren't we all travelling around in helicopters? That's pretty much the equivalent of a flying car. You could say because few people know how to fly one. But if they were readily available, people would learn. When the automobile was first invented few people knew how to drive one. The real problem is cost: A helicopter costs way more to buy than a car, and it uses way more energy so it is more expensive to operate.