The reason I find doing make up in public strange (and I'm excluding lipstick from this, because that is something that often needs reapplying and should be fast) is that I feel it shows a disregard for the person you are sitting next to.
I feel (and others are likely to disagree) that we wear makeup for other people to look at. I mean this in that we can't see our face while we are walking around, so as much as we wear it to make us feel better/more attractive/better dressed/whatever that is because other people see it. And presumably we care what we look like to those people who see it. I personally feel that to put it on in front of other people gives the impression of "I'm not wearing it for *you*, I'm wearing it for other people, who I haven't seen yet. But I will see them soon, so I want to get my makeup on before I get there". I think that this means that you (general you) regard the people who will see the makeup finished as having a more important opinion of you than the random you are sitting next to. This is likely to be true. However it is not a polite impression to give.
While I really don't care what the person I am sitting next to on the plane thinks of me, I am not going to tell them that without good cause (very good cause. Cause like cutting off an unsolicited opinion about myself that I find objectionable). I will smile and be remotely friendly. I will return pleasantries, and continue or cut short conversation as I see fit, and I will do so politely. What I will not do is ignore them as if they are nothing to me or as if I haven't even noticed their existence. I will not treat them as less than I would treat a distant acquaintance, merely because they happen to be sitting next to me.
So, there's my 2c.
And I realise others may not see it this way.