Prevailing Against The Gates Of Hell Doesn't Equate To Being Populous, Prosperous Or Popular

And I tell you, you are Peter, and on this rock I will build my church, and the gates of hell shall not prevail against it. (Matthew 16:18)

This is a pretty well known verse, among Christians because of the promise that God's church prevails in the end and among Catholics who misapply this sentence to create whole cloth the papacy. Yet I wonder if it means what we think it means. It is often referenced as requiring an unbroken line of the church existing at all times from Pentecost to today. I am not so sure that is what it means or that is what actually happened.

One of the most troubling and rarely talked about realities for Christians is that in the nearly 2000 years since the founding of the church the majority of the time there were likely very few Christians, based on what the Bible teaches us about how a man is justified. I would not say it was a stretch that for large periods of time there were no Christians and of course no visible expression of the church that the gates of hell are not going to prevail against.

Do you find that sobering and discomforting? I certainly do. I don't subscribe to the "trail of blood" theory nor do I think it likely that an awful lot of Christians believed in Roman dogma but were saved anyway. So it is likely that for decades or even centuries there was no sign of anything resembling the Biblical description of the church. Did whole generations come and go, even in "Christian" Europe without once being exposed to the Gospel? It certainly seems that is possible or even probable.

Even today, in spite of the popularity of the "health, wealth and prosperity gospel" teaching and the comfortable perch the church occupies in America, it does not follow that the promise of Jesus in Matthew 16:18 means that the church will inherently be numerically large, powerful in a worldly sense and prosperous compared to the surrounding people. That idea probably rubs some people the wrong way, it goes against the common religious wisdom of the day but I think that what we see in Scripture and church history is that the true church has always been on the margins, a distinct and often persecuted minority. 

How does that jive with your understanding of the verse in question? Does it require a substantive presence in every time or were there periods when God had His church absent from the world? I don't have a ton of answers on this one, it is just something that has been disquieting to me.