With all the talk about Lockheed's new fusion engine design, I thought I'd think about fusion's far future cousin, the Warp Engine (Federation Design). There are many similarities between the two, they both use Deuterium, they both require heavy containment physics to function, they both produce vast amounts of plasma, and they both function with naturally occurring fuel. (although deuterium has to be processed and cleaned, and warp engines technically need a supply of dilithium crystals as well.) They have many differences though, one of which is that warp engines produce substantially more energy, and the type of plasma that it produces, can be used in its base form.

But here's why fusion reactors are magnitudes better; They won't blow up everything if they fail. It has been said many times in the show that there are many, many safety measures to prevent matter/antimatter reactions from happening outside of the dilithium crystal, which can contain a reaction and allow the resulting energy to be used. However, there seem to be little to no safety measures for when the engine is damaged (other than getting lucky and ejecting the core when its about to go). Indeed, I think whenever we see a ship destroyed, it is by warp core breach. This makes the warp engine much like a big, quantum landmine that can go off with the slightest bit of provocation. What's more, is that while we only see antimatter explosions that just atomize the ship, technically they could release enough energy to wipe out a planet. That's just not good engine design, especially for something that's in use even on civilian ships. It's true that our current nuclear fission engines on ships, and fusion reactors could destroy the ship by radiation killing all the crew, but radiation can be contained, and is not instant death (usually). Even a fusion reactor, when breached, could release enough heat to decimate the engine room, and provide the pressure of a boiler explosion. You also have fusing hydrogen which would also cause mass damage. However, it would not completely destroy an entire ship or vehicle, as the damage would be fairly localized to wherever the engine was contained. You can never have a nuclear chain reaction, like that in A and H bombs, since the reaction is controlled, and at worst case, will cause what's known as a "fizzle", where uncontrolled nuclear reactions happen, but the result of which, blows apart all fuel that would be capable of causing more reactions. This fizzle has the destructive capability of the average bomb. What would happen more commonly, is that the hydrogen in the middle of fusing, likely in plasma form, would be disrupted from its controlled shape and hit the walls of the reactor, causing the reaction to be broken, and snap off like a light, while air will be sucked into the reactor, be superheated, expand, and then blow open what it has to, in order to release the energy, acting like a steam/boiler explosion.

Either way, neither fission, nor fusion could cause the widespread destruction that matter/antimatter reactions could.

You can hopefully understand now, why Matter/Antimatter engine design in the Federation is probably overall one of the worst engines you could have. Sure it produces a ton of energy, but if you were a civilian, would you really want to be strapped to something that could wipe out you and the entire system you're in, if you so much as bump it? For military vessels, I mean, fine, its dangerous, but its understandable, it would be much like the use of fission engines on seacraft in the 20th century, but there's a reason it was never used in commercial vehicles (successfully) but really, either way, given the tech level of the Federation, you think they would be able to produce good enough Fusion engines to be able to power warp coils, or at least have some sort of natural way to prevent an unwanted reaction, like nuclear engines do.

EDIT: Not to mention the fact that simply containing the antimatter is a recipe for disaster. You can blow up everything just by mishandling it!