This is a great question. I was a DRE and/or youth leader for fifteen years before I went back to school. And, now I am a scientist. One of my major professors was raised Catholic but as she says "gave up that superstitious nonsense by the time she was seven". My other major professor (I have co-chairs for my dissertation) is what can only be described as an evangelical atheist. He said to me, "I don't understand how you can be so smart and believe in fairy tales." When I was applying for one of my first scholarships, I was informed by the department chair not to discuss my religious education career and if I hadn't read anything but a religious text to make sure I read something else for the essay which was "discuss the most recent book you've read". In my cohort, came in a woman who is married to a Physics professor and was an avowed atheist and feminist. She and I met in a training conference for those of us who would be teaching, one of the discussion topics had to do with the handling the debate between creationists and evolutionists in the classroom. She was of course derisive as were many there. I said it is like comparing apples and oranges, that I was taught evolution by Catholic nuns and that there is no contradiction to the faith. The professor leading the discussion -- to my surprise -- agreed with me and seemed completely relieved that someone had finally come at it from that direction. My atheist professor in his continuous attempts to convert me asked me to read Richard Dawkins book The God Delusion. I agreed on the condition that he would read something that I gave him. Reluctantly, and I am sure without any real intention to do so he agreed. He wanted it to be less than 150 pages. I gave him Christian fundamentals and a copy of the Catechism. he gave me Dawkins book and Christopher Hitchens book God is not Good. From a critically thinking assessment of Dawkins book, it is at the best mediocre scholarship and would not pass muster in any way shape or form as a legitimate scholarly work, which made it torturous to read. We have never discussed either book. Although he recently said to me as I was leaving his office that his thinking on religion has changed somewhat in the last few years. My cohort the atheistic feminist is now my best friend and said to me one day, quite stunned, that she had never ever had a friend who was a Christian that she never bothered with them before. She has since decided perhaps she is agnostic instead and often encourages me with tidbits about my faith lol like with my husband's death, that if she believed she would tell me to trust in God's wisdom to guide me and comfort me. . .
There is a decided prejudice against being a professing Christian. Some will acknowledge Catholics are usually more reasonable and more academically or intellectually minded than other Christian denominations. A large number of the ex-Catholic and atheist members of my department came to my husband's wake and funeral and I believe they came away with a different perspective, many have spoken to me about it since then.
I think there is a secular bias against being religious on the whole and the emphases on critical thinking, the scientific method etc can call to and satisfy those who were raised in a purely secular way. I also think there is a status sort of thing with being above religion for some people, for some I think it is a continuation of typical teen rebelliousness and is little thought out but pretty vocal, they will spout Dawkins' quips and think they have scored some zinger, but they couldn't argue it out and luckily for them Dawkins suggest entertaining such dialogue is a waste of time -- convenient for him and those like him who can then continue in their poorly reasoned belief.
My deacon just gave me a copy of John Hough's Science and Faith a new introduction. I just started it but I think I am going to give it to my major professor afterwards to read.
I think those who are struggling on their path can be sidetracked by the secular arguments in academia. I think many can also succumb to the rather blatant prejudice against those who profess a faith. It's wrong to be against someone who is Jewish for that would be anti-semitic but it is perfectly alright to be anti-Catholic or anti-Christian. As if their academic prowess has somehow shone them the error of religious thinking, but they forget that they would not have much of the academic foundation they currently have without those same devout men of faith who founded and taught and made discoveries and did science. My own field is full of monks and priests. It is very similar to Protestant Christians who are decoupled from their religious foundations for none of them would be here today without the foundation built by Catholics, many are so disconnected that they don't even know their founding history -- for example many are surprised to learn that Martin Luther loved the Holy Mother and wrote some of the most beautiful prayers to her and did not deny the Immaculate Conception nor the Incarnation.
So, yes it can be very difficult to maintain your religious belief in the face of opposition to it in academia and the sciences but not only the sciences. But, holding fast can be beneficial to the others as well. And, for those not prepared to defend or explain their faith it will be most difficult which is why catechesis that also provides apologetics is important. They will find arguments they are unfamiliar with and derision etc. I don't know which is worse the ex-Catholic or the never believing, but I have found that both have a marked lack of true knowledge or understanding of that which they deride.