Agent Smith was a representative of the Architect and as such he had a very poor take on the human beings, which is to be expected. However, Agent Smith clearly did spend some time working out his theory that humans are a virus all on his own. And he is correct, at least in terms of the logic that he sited to Morpheus. In his thoughts on the question he sited the fact that all species on Earth, save humans, breed only to the limits of the resources at hand. Viruses continue to multiply until there is nothing left to use for survival. Humans have, most certainly, behaved more like a virus than a mammal in that regard.
There is, of course, no argument that humans are, in fact, mammals. We are of that genus and that's all there is to it. But, Agent Smith's comments were based on displayed behavior and he couldn't have been more right. China has, as a result of it's own overpopulation, now mandated that each family in the country may have only one child. The government has recognized the need to control their numbers in order for the country to be able to support it's populace. While the idea may seem wildly extreme to us in the States it has been deemed as necessary by the Chinese government to check the unbridled growth of it's people. While China isn't the only country to practice this "virus-like" breeding behavior they are the only ones to have taken government action in order to control the problem.
This planet has a finite amount of resources that we can make use of in order to survive. We seemingly have no concern about this as families continue to churn out children at alarming rates. Often times the people least able to afford large families are the ones that have the most children. There is a practice that speaks to the very point that Agent Smith makes in his thoughts on the human condition. Those on welfare or that hover at or below the poverty line very often, though not always, seem to have the most children to support. Setting aside the thought that it is a working class stiff whose tax dollars go towards the support of those children, it is the behavior of a virus to overpopulate a system, take it over and in the long run kill it. There is most certainly a case to be made that this behavior is vastly different from most other mammals on the Earth and very much more like a virus.
Looked at another way, humans have brought about the most alarming negative effects on the Earth's ecosystem. When other mammals are left to their own devices they tend not to destroy the places that they call home. We tend to destroy everything we touch in the name of progress and growth. We leave nothing untouched or untampered with lest there is some law our government makes to protect a thing we might otherwise harm for sake of our own immediate needs. We have a global warming problem that threatens our survival and yet we have American car makers bickering and whining about the new miles per gallon averages that the government wants to force on them. One wonders at the thinking the automotive industry practices when they see gas prices at their current high levels and see that the reserves of oil dwindling.
Humans are a virus. A virus that has plagued the Earth and made it very sick. We, if allowed to go on unchecked, will surely kill this planet with our use of fossil fuels, global warming and all manner of pollution. We should, no, we must heed Agent Smith's logical conclusion that regardless of what we really are in terms of genus, we are most certainly behaving like a virus. A damn virulent one at that.