Determining what church a family member attended depends on when that relationship began. The further back in time the less organized a majority of churches were. Though I found the name of the pastor whom married many of my ggggg-grandfather Adam Smith's children, I could not find in the late 1700's and early 1800's what particular church he attended, despite knowing his faith. Finally after reading local Shenandoah Valley history, I came across some information of how the German Baptist were attempting to convert Quakers in the area. The section mentioned that the early congregations went from individual homes to conduct sermons and services. Soon a picture arose of how some early denominations did not have a single church building to congregate. Such churches had poor record keeping. If it were not for county records of marriages, most of the records would have never been found. Another example was the discovery that the church my mother's family attended in North Carolina was torn down to make way for a reservoir.
Thus it becomes imperative that a researcher must read the history of a given area in order to gain clues and insights about the congregations a relative visited.
Early areas were often segregated by not only ethnic lines but also religious beliefs. Most counties and townships in the central and western states have histories which were published in to large one of a kind books around the turn of the 20th century. Often they concern the history of the individuals and churches and are broken down into townships. A majority of my family's religious history were in such books. Ask the genealogical group in the areas that you are interested in, about such sources.
Sometimes local churches of a network of churches pooled their records under one regional location. You can easily find any denomination online. Some of these churches have a website. One source is under genealogy.com in the article "Locating Church Records". The author lists sources of church records for each state. The LDS church and it's site FamilySearch.com has some of the major church records
When you find a church member whom is willing to take the time to search records, don't forget to give the church a donation. These institutions are filled with volunteers and locating records are in their hands.
We have often heard that we should not talk about religion or politics at social gatherings. But, finding out what church uncle Joe attended, may open a whole new source of history about him and your family.