I am Jewish, and live in Israel. I have travelled on Emirates and visited both Dubai and Bahrain (on a UK passport) without any problem at all. If you're orthodox, expect a few customs questions about your phylacteries (tefillin) but nothing untoward. I experience only friendship and iterest there. I felt much more unsafe in Lyon and Cairo.

Regards

PS - If you keep kosher, don't expect a KSML on Emirates - take some sandwiches!