The overall argument in The Botany of Desire is that plants control us just as much as we control them. That is, they access our desires—for sweetness and beauty and pleasure—in order to ensure that we will care for them and help them propagate. The relationship between us and them is, thus, generally symbiotic.
In Chapter 3 Pollen examines how marijuana appeals to an innate drive to experience other forms of consciousness. While it grows naturally in the wild it appealed to our desire for an altered consciousness so that it could be better cared for in places like indoor greenhouses and well-fertilized farms.
Here Pollen is not explicitly making an argument about whether marijuana is good or bad—he calls it a poison yet admits his attraction to it (117). On the surface, he is merely saying that the plant—despite its down sides--has been effective in attracting us to it enough that we will help it grow. Implicit in the chapter, however, may be an argument that marijuana is attractive enough to stay.
Part of his argument is implicit in the structure of the book. He’s included the chapter on marijuana amongst those about accepted plants like apples and tulips and potatoes.
In making his case, he goes all of the way back to the Old Testament where there’s “a connection between forbidden plants and knowledge” (120). Here he’s referring to apples, but because he doesn’t make that explicit he gets away with a metaphor whereby marijuana is cast as being no more harmful than an apple.
He also compares the plant with wine and beer. Indeed, on p. 122, the Greek god Boethius is mentioned, along with Greek feelings about this god as merrily ambivalent.
In other places he calls them “jolly green giants,” further highlighting their dangerous but not so dangerous nature (122).
Elsewhere, he asks rhetorical questions, like “did marijuana pose a grave threat to public health?” for which we can guess the answer is no (127).
Again, however, Pollen is less explicitly concerned with arguing the political question than in showing how the plant has shaped us. In doing so he traces the plant from individual gardens to indoor greenhouses to university labs (152). He claims that the plant changes our biology and returns us to a state of “wonder” (168).
If you look at the quotes I've provided, however, you'll see that implicit in his langauge is an argument that casts marijuana as dangerous, but not as dangerous as we might have thought.