How to refute an argument based on “It makes me feel good what’s wrong with that”?

If the argument is "homeopathy cures illnesses" then for me that's something worth debating about.
If the argument is "believing in homeopathy doesn't cure me but makes me feel good, so please don't burst my bubble", I would not say anything more.
Note: The counterargument with painkillers is that taking drugs in general is harmful because the liver has to work to neutralize them + drugs have side-effects  - a doctor would be able to give a better explanation, but I'm not a doctor. So the analogy of homeopathy and painkillers is I believe a weak analogy. Relying on homeopathy, though, for serious illnesses and refusing traditional medicine is harmful . And again saying that "believing in homeopathy makes me feel good" expresses how someone feels and people's feelings are not debatable. 
The claim "Homeopathy cures" is not a fact and anyone who says that should provide evidence or stop spreading misinformation because it's not true and that COULD BE harmful (at least economically).

Someone told me that if thinking homeopathy makes them feel better why is that bad?

The problem is that feeling better =/= getting better. The placebo effect of homeopathic medicine (and other pseudoscientific treatments) means that, although they have no health benefits - and might even be harmful - the patient might feel as if their symptoms are easing up. This masks the fact that the 'cure' did absolutely nothing, and might even cause them to reject legitimate medicine which would actually help.

The general response is usually that I’m making an equivalence or I’m arguing in “Bad faith”

The term 'bad faith', and the phrase "you're acting in bad faith", are often swung around haphazardly by people who don't know what they're talking about, simply because someone questioned core assumptions in their argument. The logic is that those assumptions are self-evident, so only someone with bad intentions (e.g. debating for the sake of it to wind people up) would criticise them. It is rarely the case that those assumptions actually are self-evident - they might even be false, as in this example.

So you're not arguing in 'bad faith' by asking why someone would take a useless 'treatment' to help with their pain. It's the question everyone should be asking, actually.

I noticed perhaps when I push an argument to absurdity maybe it comes off as condescending or equivocating.

This isn't to do with logic, fallacies or reasoning, but there is a chance your tone is off-putting (e.g. the occasional snide remark, or maybe you're being blunt - I have this problem too). Then again, you might also be trying to be polite as possible, and the other person is just unreasonably refusing to listen to a sensible second opinion.

How to refute an argument based on “It makes me feel good what’s wrong with that”?

Generally this is OK as a justification for trivial things, but for more important things (e.g. getting married), one should sit down and consider alternative possibilities and evidence.