Which airlines might I have trouble taking, being an Israeli?

I'm an Israeli expat living in Europe (proper residence etc. but no citizenship/passport). I intend to travel from Europe to India, and I'm considering using an airline based in a state without diplomatic relations with Israel, which may or may not be somewhat hostile to it (e.g. Emirates but not just them).

My questions:

Will I have problems with my specific choice or can I just safely book the ticket?
More generally, how can I tell which airlines might be problematic for me to fly with, using an Israeli passport, and assuming I fly between places through which I can pass with that passport?

Notes:

Please do not interpret this question as trying to legitimize or smooth out issues stemming from problematic Israeli policies; I have strong political opinions (dissenting by Israeli standards) on these matters which I will obviously not go into on this website, and am not passing judgment this way or that, for the purposes of this question, on airlines not taking on Israeli passengers.
Answers regarding transit stops are relevant.