As humans become more and more dependent upon medication for survival, we can expect the human immune system to slowly weaken. The best way to explain this is with an example using hormones: imagine a future in which, with the help of supplements, you can regulate your hormones to maximize your wellbeing. Over time, your body would become dependent upon the additional hormones, to the point where it might stop doing for itself what the supplements can do instead. The processes which create hormones would become less important for survival, since your body would always have enough, thanks to the supplements.
After tens of thousands of years, it is likely that humans would evolve to the point where hormones are no longer created organically within their body. Taking this example a little further: if external aids were entirely responsible for our survival, many of our internal functions might become obsolete. Why would your body need a powerful immune system if all pathogens are tackled with medication? Indeed, it is but another downside to the use of medication to fight diseases.