Don't you have that problem with any energy-dense fuel? It's just that it doesn get more dense than that, so you can be very space and weight efficient.
It's like everybody saying that a hydrogen car is a rolling bomb because of the energy stored in the hydrogen. Well, sure, but gasonline has just as much energy stored. Which is the whole point of fuel. To store energy. It's not like you are bringing 100x as much energy with you just because it's hydrogen. So that doesn't make an ICE car any less of a bomb...
The difference is that antimatter annihilates with any normal matter that it comes into contact with. This means you can't just put it in a tank, the way you can with hydrogen. You can't e.g. combine it with some metal to make a metal hydride to make it safer to store, the way you can with hydrogen.
At an absolute minimum, you need extremely strong magnetic confinement and an extremely hard vacuum. And even then, you're going to get collisions with stray atoms and annihilation events which release gamma rays and other radiation products - although shielding is probably the least of your worries in this scenario.
A typical research lab at a university or large corporation can't make a vacuum strong enough to store even tiny quantities of antimatter for more than a few minutes, and they can't produce the magnetic confinement strength required to store macro quantities of it, either.
So the question with an antimatter-powered car is not if it's going to destroy the surrounding region and bathe it in hard radiation, but how many milliseconds (or less) it will take before that inevitably happens.
But probably luckily for us, this is all moot, because we have no way of producing enough antimatter for this to be an issue. If all the antimatter that's ever been created by humans annihilated simultaneously, only scientists monitoring their instruments closely enough would notice, because it's such a microscopic amount.
Edit: for perspective, you'd need about 7 billion times the 92 antiprotons transported in the truck in the story to produce the energy produced by a single grain of gunpowder.
Also, now your tank is just fuel as well.
Liquid gasoline does not spontaneously explode like an action movie. You can put a match in the fuel tank and (presuming infinite oxygen availability) it'd just start a small fire. Heck, may even just give a little puff and then put out the match.
Antimatter in any sufficient fuel quantity, the moment it breaks confinement, will completely annihilate and release ALL it's energy in a single moment, setting off a chain reaction to the remaining antimatter. It's like sitting on an armed nuclear bomb, where you rely on electrified, highly sophisticated containment equipment never failing a single time for months to years... In a radiation-heavy environment known for causing sophisticated electronics to have errors.
And, yes, hydrogen cars were looked at critically because of the perception they can Hindenburg (I'm unsure if it's true or not). Which is a good example because you don't particularly see any hydrogen blimps anymore - we made them illegal because they're dangerous.
Batteries have some of these same risks: they store a lot of energy and it can be released very quickly under the wrong circumstances.
And, no, batteries can have outbursts but they're nowhere near as catastrophic as compressed, explosive gases or an antimatter bomb.
The practical limit for nuclear energy is about 5 to 10 times less than that, because the theoretical limit corresponds to the transmutation of hydrogen into iron, coupled with the capture of the entire energy, which will not be achievable any time soon.
But there is an essential difference between nuclear energy and antimatter energy. Nuclear energy is stored in our environment and you just have to exploit it. Antimatter energy is a form of energy storage, so you need some other form of energy to make antimatter. The energy efficiency of making antimatter is many orders of magnitude worse than the factor of less than 100 that exists between nuclear energy and antimatter energy and the mass of the confinement device needed for storing antimatter is also orders of magnitude greater than the mass of the stored antimatter.
For now, there is absolutely no hope of ever using antimatter in practice for storing energy. Such a thing could be enabled only if some technologies that we cannot imagine would be invented.
Despite the great technological progress of the last couple of centuries, it is hard to say that there have been many inventions that have never been imagined before. After all, already 3 millennia ago the god Hephaestus did his metal smith work with the help of intelligent artificial robots.
With antimatter the tiniest leak will annihilate your ship.