Starting in grad school, I often found myself the lone dissenter among highly educated, well-spoken likeable people, only able to maintain my beliefs because I had previously established an intellectual foundation for them. I anticipated changing some previous theological and epistemological ideas due to my graduate school training, but engaging in deep thinking about my Christian faith before graduate school made sure that these changes were well thought-out.
The anti-Christian discrimination we see in the academy does not give Christians an excuse to give up on the pursuits of scholarship, research, and higher education. It becomes too easy to look at potential episodes of prejudice as a reason for our failures. As an African-American, I have seen this attitude in some blacks, and as a Christian academic, I can see it in some Christians. We do better to assume that most people want to be fair. I honestly believe this to be true. Academics tend to advocate religious neutrality. This stated value makes it more difficult for those with anti-Christian animosity to overtly act on that animosity. This is not to say that religious prejudice and discrimination will not take place, but appeals to religious neutrality usually keep much of this discrimination in check. Keep plugging away and strive to succeed even if you suspect anti-Christian prejudice. A fatalistic attitude because of potential prejudice can hijack your career before it gets started.
Expect that you will have to perform better than non-Christians if you want to succeed. Research that does not fit in with the general social values of secularism will have a more difficult time getting published. I've done work in the area of race, which fit into the general social and political paradigm of my field, and on anti-Christian hostility, which did not fit into that paradigm. It's been much harder to publish on the latter. There is a general expectation of excellence in the academia. As Christians, especially when working with unpopular topics, we must strive to be even more excellent than our peers. Meeting this higher standard can help Christians have an impact in academia.
Finding social support is critical for Christians in academia—particularly when in graduate school. Many of your fellow graduate students will not understand your faith, and most Christians will not understand your academic and unique social challenges. If possible, find a local community of Christian academics and graduate students. If there is not such a local group, contact Grad Resources, which can supply material and possibly help you find mentors. If you know of a Christian in your field and admire her work, do not be shy about reaching out. Part of a scholar's job is to mentor younger scholars, and a Christian scholar should be especially willing to share her time. Selection of your advisor in graduate school is also important. It is great when a Christian can find a Christian professor to be his advisor, but that is not always possible. However, it is wise to steer clear of an advisor who shows a high level of anti-Christian animosity. A bad advisor can rather easily sabotage a student's career.