Make the plants hard to eat, both while alive and after death.
This can be simply tough molecules -- trees can take centuries to decay even on earth -- or heavy metals, or toxic compounds.
Such animals as manage must cope with this by not growing too large and requiring more food than they can cope with.
Trees evolved to have more access to light, as a taller plant can cover a smaller plant, and remove its competition. Without light, this strategy doesn't work, and so these chemotrophs will most likely not evolve to become trees