Humans sure like to think they are in charge. “Being in charge” can be considered being able to eat and survive. Feeling the need to take the dominant role amongst all species on Earth, humans thrive off the sense of power and control over everything that goes on. This especially comes into play when dealing with hierarchy and the food chain. According to humans, humans are the highest on the food chain whether this be because humans have the ability to use weapons (guns) to overpower any other species that is acting out of line in the food chain. Perhaps this is enough evidence to support the fact that yes, humans are in charge.
For a very long time humans have hunted and killed animals for food. This trend seems to have always been and will always be the case. Very rarely is this relationship reciprocated but it has. Every once in a while a zebra may kill a lion. When the species lower on the food chain overcomes the higher species, fear is a likely factor and the lower species was simply acting out of fear, not to hunt the higher species. Humans appear to be more sophisticated than other species, or at least more sophisticated regarding the methods for hunting and killing for food. Elephants are not shooting guns or using a bow and arrow to obtain their food. Based on this sophistication, humans can be considered in charge.
There are more similarities between humans and other species than differences that separate humans from other species. Species of the same kind are able to communicate to one another, as seen in Blackfish amongst the orcas. Species are able to build and take advantage of their resources, as seen with birds building nests or beavers building dams. But other species are not able to melt metal or process and package food into plastic. Other species can only do so much while the possibilities for humans are far greater and more promising, especially when it comes to survival. There is not another known species that can do what humans do.
Maybe there is not even a contest between humans and other species. There could be dualism where humans and some other species are both in charge, but in completely separate brackets. Maybe humans cannot even be compared against other species. Humans may be in their own category by themselves with no one or no thing to compete against. From this point of view, it is almost not even fair to debate whether humans are in charge when all that can be compared against humans are animals.
Humans being in charge may happen without human agency. Perhaps humans were just made to rule the world and have dominance over all other species. It may be merely human nature to instill fear in other species. I wonder if, say 500 years from now, how other species will have adapted to humans and if humans are still in charge. It is weird to think about but nothing can be ruled out or impossible.