Is it ok for Chili pepper plant's fruits to fall into its soil?
As @MCM says, the capsaicin molecule isn't intrinsically damaging - its effect upon us is mediated through the TRPV1 (Transient Receptor Potential Vanilloid 1) receptor in the membranes of cells whose function is to sense noxious stimuli such as heat. The binding of capsaicin to this protein causes transmembrane movement of Ca2+ ions which depolarises the membrane, triggering an action potential - a signal to the brain. Heat has the same effect on the TRPV1 protein. In this way the presence of capsaicin mimics the effects of heat, causing a painful sensation.

Have a look at this SE.Biology question.