It seems to me that God is more concerned with the depth of a church than its size. Some churches, following some formula that a "church consultant" came up with, no longer talk about "the blood of Christ" because it *offends* some people. IMHO, some churches need to be "preached-down" to the core through the teaching of solid truth.
You are right. It is not the size that should be of concern as much as what is being taught and lived by every day. The bottom line is this: we need to be in the church family that God leads us to be a part of. If that happens to be a large church that is okay. If you feel led to be an active part of a smaller church-go for it!