As a Jew, I've definitely had some conflicting experiences, but they've definitely been more internal than external. I haven't really been affected by any anti-Semitism (the only time this occurred, I was able to initiate a discussion with the person and hopefully changed their preconceived notions about Jewish people), but there's definitely a subtle mindset within the community of persecution, especially when a member of the community does something illegal or downright disgusting. I find this disturbing - both that the actions of a few members of the community can have a effect on the mentality of the whole, and that in today's age, in a comparatively liberal country like Australia, we're still maintaining that paranoid mindset that was even more prevalent in European and to an extent Middle-Eastern communities over the past few centuries.
Personally, I consider myself an Agnostic Theist - I 'believe' in God (but I believe that to state that God 'exists' is contrary to the Jewish interpretation of what God 'is', but that's another discussion), but I'm certain that no empirical or falsifiable evidence either for or against God's 'existence', hence I feel that any serious discussion or debate as to the 'existence' of God is moot. Regardless of this, I'm still a practicing Modern-Orthodox Jew.
Regarding OP's point; I do believe that religion often has a negative stigma attached to it today. It's seen as being contrary to the progressiveness, as well as the fundamental evidence-based nature, of science. However, as someone who is both religious and studying the sciences, I see no conflict whatsoever - in Judaism, or at least in the interpretation I was brought up with, learning is encouraged regardless of its nature and to fail to question everything, both in the secular and Jewish studies, is to have missed the point of learning. I guess in that sense I don't find it difficult to be religious in today's world - rather I feel more comfortable today knowing that I can fulfil both my religious and my secular duties without them being in conflict with one another.
I also believe that the most damaging people to any religion are the zealous, ultra-religious factions or individuals. In Judaism, many of the Ultra-Orthodox communities isolate themselves from the outside world, they (in my opinion) mistreat their women and they are often radical.
This is an example of the radical ultra-religious groups I'm talking about.. These people do, and will do, so much more damage to religion that any atheist could - they denigrate their religion in the eyes of God, other less radical members of their religion, and the general population.
P.S. Florian and Alex, I'm amazed and extremely happy you called it a kippah instead of some crazy Yiddish word

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Sorry for the rant, OP - I'm pretty sure I went off topic a few times - but I have so much to say about this that I couldn't even begin to put it all in one post.