There's a really good book out there by Stan Grenz called
Renewing the Center where he talks through the historical movements that led to the situation in post-World War II western institutions that questioned the basic beliefs of Christianity.
Anyways, to get to the bones of it...you can trace the start of this back to the German theological schools. Following the Kantian revolution (you can't get away from Kant in western history) another philosopher/theologian arose named Schleiermacher. He changed everything. Between the two a massive intellectual shift began occurring in western culture.
Now, because the US was isolated from these movements by a fairly large body of water, the shift never made it to the eastern shores of the fairly new country. Well, it made it but it didn't have much impact.
In Germany and France the shifts were absolutely massive. The growth of the German Liberal tradition (we use a capital "L" for a reason) began out of the end of these two men's lives. With the explosion of Cartesian Modernism in Europe, coupled with the growth of continental philosophy, the idea of absolute certitude became king.
So, many theologians began digging deep into the Scriptures to ensure that we had a proven, absolute biblical text. Imho, they started off with good intentions. However, they had a terrible time of it because neither science nor archeology, and not even linguistical theory, had evolved to the point to truly offer answers to many of their questions. At the end of the 19th century, several schools arose as principal chairs for the theological growth and shift towards modernism (or what we might call liberalism...little "l.")
By the time the Titanic sailed, the German Liberal school had won the day in Europe and we would see the slow demise of a Christless, baseless, groundless Church. There's a reason so many churches and cathedrals are empty. They emptied themselves theologically first...the people soon followed.
So by the time the Titanic sailed a new school of advanced theologians was arising. The major theologian of the time was Wilhelm Hermann. Hermann had two significant students: Rudolph Bultmann and Karl Barth.
Long story, terribly short...Bultmann became the greatest exegete of last century. He also became the greatest theological liberal of last century too. Barth was headed down that same path, though his field was systematic theology...or dialectical theology. But Barth changed.
Anyways, by the end of WWII the ship of liberalism had sailed and many of the primary institutions in America were filled with German and French scholars and students of scholars. The major institutes and seminaries all changed for the most part. I think of where Union was and now is, the same for Harvard, Yale, and several others.
Once the 1960s came, the whole Christian theological system was up for grabs. Nobody believed in any of it (mostly thanks to Bultmann's demythologization.) And an entire generation of scholars working in schools accepted denials of the resurrection, Jesus as a historical figure, and many other core doctrines. In secular studies, Christianity was seen as a bunch of primeval wackos.
However, Habermas is right btw, the tide is shifting.
Because of the growth in linguistical theory, some archeological data, and time to work through many of the problems presented by the German Liberal school, we've been able to establish some core beliefs and doctrines as legit. It took a generation to catch up (probably due the after-effects of the failed Fundamentalist-Modernist controversies) but orthodox Christianity is one of the most well supported religions historically.
Even agnostic scholars like Bart Ehrman accept that Jesus lived on earth and died by crucifixion. This shift is due to significant research and people who dedicated their lives to answering parts and pieces of the questions thrown at us.
When I think of scholars like Hurtado, Plantinga, Bauckham, Wolterstorf, Wright, etc etc etc who have re-established the core positions of Christianity in their own unique ways...well, there is a greater day ahead.
This doesn't mean its all bells and whistles through the academy in 10 years. That isn't going to happen. However, it does mean that we have an increasing body of literature, scholarship, and research that supports the basic message of Christianity and scholars both religious and secular who back this stuff up.
We are amid a really interesting time.