Well you don't have the uncomfortable feeling, because you rationalize it away by declaring coffee (caffeine) something entirely different from (other_ neural enhancers (in pill form). Cognitive dissonance is, like you say, the uneasy feeling of having two conflicting views at the same time. Your are 'pills are bad' and 'coffee is ok'. (If I may speculate, I'd say the both come from social conditioning, or rather, accepting the mainstream or conventional views on these issues without thinking about them critically. For which nobody can really blame you, I mean if everybody had to second guess every single thing we see every day ('regular' people drinking coffee), we'd get nothing done at all.)
Anyway so those are the two views, but when you link them through 'they're both cognitive enhancers', a problem arises. Why is one bad, and the other not? So this is then 'glossed over' or 'smoothed out' by the brain by internalizing a third cognition, namely 'they're not the same'. Note that this third cognition does not have to be elaborated on very much (actually this elaboration is what I asked for, because I don't think any argument in it can hold) to put your mind at ease and 'resolve' the cognitive dissonance.
Anyway, my point still stands. I challenge you to explain what is the fundamental difference between taking a chemical in pill form versus taking it in liquid form (this is what it, in my opinion, boils down to). I guess the most obvious argument is going to be that one is man-made and the other 'natural' (which somebody arguing this then usually interprets as "the precursor is readily available in nature, and extensive treatment in the form of drying, grounding, and preparing with hot water is 'pure' enough to all be 'natural".) I won't put any words in your mouth, I'm just pre-empting the usual first response and indicating what I see as weaknesses in that argument ;)
Finally, for the record, I didn't downvote you as far as I remember, but your comment did rub me the wrong way. The reason being that it states a very strong opinion or position, but offers nothing to rationally substantiate that opinion. On the contrary, the only attempt at convincing the reader seems to be in a 'proof by assertion' strategy, repeated across multiple posts. Furthermore from your claim that people only downvoted you because you hold a different opinion it seems that you are not very willing to critically examine your own position, nor to put in the effort to really (as in, rationally and in a dialectically sound way) defend it. I hope I'm wrong on this of course, I'm just letting you know how these couple of posts came across to me, hoping that this may help you understand why people reacted to your post the way they did (well, 'people', just 3 really, but still).