Since your question allowed for the presence of antimatter technology but just not the usage of antimatter weapons, I am going to go into various things that will let you keep your antimatter reactors but avoid the bombs, or at least make them less deadly.
Antimatter energy release is in the form of gamma rays
A lot of what follows hinges on this fact.
Well, not exactly, but some of the other stuff decays right away into gamma rays too. For practical purposes, we can just say that the energy is all in the form of gamma rays, and that approximation will be sufficient.
Gamma rays are electromagnetic radiation of a certain frequency. The antimatter EM radiation will all be at a particular frequency.
Metamaterials bend light, and different materials work better for different frequencies
Metamaterials are used to bend light around objects. Usually, people think about them for their potential as a cloaking technology. Right now, we don't care about staying invisible... we just want to stay alive in the era of antimatter bombs.
Your people could have a metamaterial which works amazingly well for the particular EM frequency that makes up an antimatter bomb's blast. Although an antimatter bomb packs a huge punch, that punch won't be so bad if it goes around you. Put these on all your space ships, space ports and buildings, maybe even your ground vehicles.
Antimatter, whether bombs or batteries, might be easily detectable
Others have stated why antimatter bombs are not feasible because of things such as their massive containment requirements. You could use that in a different way.
Contained antimatter in your world could be easy to spot because of its huge containment facilities. It could also be detected by sensors looking for its gamma ray signature - heck, there could be dedicated satellites that allow the government to always know where all antimatter is at all times.
So you say your bad guy has put something around his antimatter containment to block the radiation so it's not detected, so he can move his bomb and sneak it into somewhere? Everyone sees the ridiculous attempt because you can't hide a huge, moving antimatter containment vehicle, so there really is no way to get away with it.
Antimatter bombs are not as dangerous as people make them out to be
Don't get me wrong; there is a colossal, unfathomably huge amount of power to be released from even 1kg of antimatter, and I would not want to stand next to it. However, because of the way that the energy is released practically all as EM radiation, a lot of it will be spread around more or even lost out to space.
An antimatter bomb might release a lot more energy than a nuclear bomb of the same fuel mass, but a lot more energy will be wasted too. So antimatter bombs are not necessarily the best weapons.
You might as well not worry unless you're going to worry also about similar problems
As mentioned above, nuclear bombs do a better job of transferring their energy to their immediate surroundings in a manner which destroys things.
Even discounting nuclear, there were huge bombs even before, but they just happened to be massive amounts of chemical bombs.
So whatever your response is for those, you can just do the same for antimatter. If you're just not going to mention nukes or other things, then just don't mention antimatter weapons either. If you are going to go into a big deal about why antimatter weapons aren't available, then you kind of need to do the same for those other things too.
Unless antimatter batteries/reactors are a big part of your story, then that makes more sense.
It has been discovered that you cannot make a reasonable antimatter WMD
This one is slightly more made up, but it sounds so reasonable that it would require little to no suspension of disbelief...
When you contain your antimatter as a gas in a magnetic trap, some atoms escape if they get too energetic or if a normal matter atom makes it in to annihilate with them. The more antimatter you have in one dense spot, the more this happens. There comes a point at a high enough mass where long term storage is not reasonable, and this point happens to be less than the mass required for a weapon of mass destruction.
So there are no antimatter weapons because you cannot keep an antimatter weapon viable long enough to use it.
Fortunately, even small amounts of antimatter are useful as batteries. Also, even though a large mass of antimatter cannot be kept together reasonably, that doesn't stop you from having multiple smaller amounts near each other... not suitable for a bomb, but suitable for energizing a system and replacing with fresh antimatter periodically.