In my outbreak story, the main focus is the zombie survival in the quarantined state. These zombies cannot take out the government, but rather weaken them greatly. In my story, there are bad humans and all of that, but I do not want to make the theme be about humans being worse. How could I make it so that while there are human enemies, the zombies are still the main focus?
This question could be considered borderline 'what to write', but it could be read as relevant for any question of antagonist(s) and balancing.
It is your world -> You make the rules.
You could simply make it so that perhaps:
1: Humans often "need" each other more than they are a threat to each other - when they run into one another, they may make trades, etc.
2: Your world is so greatly affected by the zombie apocalypse, that people rarely actually run into other 'normal' humans. This would make the zombies the main threat.
1 and 2 do not rule out each other.
Generally, the way you design your antagonist(s) will lead to a natural balance of the threat(s) they represent.
Humans: If you limit resources, humans will be more desperate, making them more dependent on fellow humans; either to collaborate with or to take advantage of. Their desperation could make them less stable and 'dangerous, but a lack of resources would probably also make them less well equipped to be a threat.
Zombies The way you design your zombies will determine how great a threat they are in general. They way you design the environment will determine the interplay between humans and zoombies.
If you want two antagonists--the zombies first and the humans second--make sure the threat of zombies is greater than the damage that humans could do. Whenever your protagonists are worrying about humans, make their thoughts gravitate back to the looming danger that zombies could do.
You can also produce 'targets' for both enemies. Yes, both are antagonists, but make the target that zombies threaten even more important than what humans could do. For example, maybe the humans are trying to put your protagonist in jail. That's pretty bad, but what if zombies are moving towards the extinction of mankind? Right away you have put the proper antagonist in focus while still maintaining the 'antagonist-hood' of the humans.
Everything around the "bad humans" has to be a sub-plot.
Your characteres must have a clear goal related to surviving the zombie outbreak (i.e. reunite with their families, find a cure, just the sole desire to live...). During their journey they will encounter both good and bad people, but all of them have to be either obstacles or aid on their surviving. In other words, your characters will have to remain focused on surviving, and shouldn't change their mission to stop the rebel group that wants to overthrow the government, or unveil the evil corporation that is behind the outbreak, or prevent the military to use zombies as weapons... All of that COULD be happening in the world, and your characters can participate, but it still has to be just part of the journey and not the end goal.
Your society probably doesn't fight amongst themselves because they can't afford it. There's so few of them they can't afford petty squabbles. A zombie apocalypse is the perfect breeding ground for a tyranny or a dystopia, why not just create a harsh government where killing zombies is their only mission?
Zombies Create a Common Enemy
"Zombies are the root of all evil. We've all lost someone to them, mothers, daughters, sisters, brothers, fathers, sons, and lovers. That's why we need unity in these dark times, a beacon of light to pierce the darkness. We'll wipe these undead abominations off the face of the Earth no matter what the cost." -General Arthur C. Burnhouse, leader of the Zombie Annihilation Union (ZAU)
When the world fell, the people were hopeless, scared, and lost. The old government had collapsed or fallen into disarray, but some remnants of the military survived. The new forces were led by one man, a general who was far more ruthless than any other, one who was willing to get the job done.
He lost his family to the zombies, so he was driven by only two goals. He wanted to keep humanity alive and destroy every last zombie he could find.
Since the world was in chaos, people flocked to him and his soldiers for strength and support. Those who were strong enough to fight were added to the general's forces, and those who had valuable skills such as medical knowledge for curing wounds or scientific knowledge for developing a zombie cure were all put to work in his forces.
Anyone without a specific use either had to pick up a useful trade fast or risk getting left to the zombies. There were dissenters in the ranks, at first, and there were rival factions too, but the general was quick to stomp them out. He would not have disorder. He would not have anyone threatening the survival of humanity.
The government had its flaws, but zombies were the perfect scapegoat for all the regime's problems. The general had a silver tongue. He knew how to stoke the fires of people's hatred to a billowing blaze, so he did exactly that. He never let people forget their fury towards the zombies.
Every day the people were fed line after line of his propaganda until every last person was so brainwashed against the outside world that they only knew loyalty. Zombies were the enemy, and the regime was good. Nothing else mattered. They would live and die for the Union. That was their only purpose.
Every time the zombies broke through and killed someone else, it only fed the people's hatred just a little bit more and proved the General more and more right in their eyes. This was an enemy that could not be reasoned with. This was not an enemy that they could fight alone.
"Either we fight as one or perish as many." -Beginning of General Burnhouse's most famous speech.