There are three main positions within Christianity on general alcohol consumption: moderation, abstention, and prohibition. In general, high churchmanship correlates with moderationism, while lower churchmanship correlates to taking a stronger position against alcohol.

In general, abstentionists argue that alcohol is permissible if there is no other way to effectively purify water, as was the case at the time, but that Christians should avoid unnecessary intoxication.

Part of this is a class issue. The most high-church Protestant denominations are Anglicans. In the US, the Episcopal Church (the main group of American Anglicans) has traditionally been associated with the upper class, while low-church denominations correlate to lower classes. This obviously leads to a different perception, between the rich people enjoying their fine wine under the knowledge that too much would deprive them of reason and the perception of alcohol being a foul-tasting liquid that exists only to turn men into worthless layabouts. This is apparent in the earliest stages of the temperance movement, when temperance activists primarily focused on distilled drinks, sometimes even advocating the consumption of beer or wine as an alternative (as in William Hogarth's famous pair of paintings Gin Lane and Beer Street).

The main period in which anti-alcohol sentiment increased was the Second Great Awakening and the Holiness Movement. A common strain here is that since alcohol often leads people to sin, it is itself inherently sinful. Therefore, manifesting holiness involves separating yourself from it completely.

Part of this comes from differing sacramental theology. While Catholics and extremely high-church Protestants (mostly Anglo-Catholics) believe that the bread and wine of the Eucharist physically become the body and blood of Christ, most Protestant denominations (including the majority of Anglicans) teach that Christ is present in the Eucharist but do not teach that the bread and wine physically become the body and blood in the same way, with a common explanation being that Christ is spiritually but not physically present. The form of presence generally gets further from Catholic-style transubstantiation as churchmanship gets lower, with most Baptists believing it to be purely symbolic. Because of this, it is easier for people in lower-church denominations to justify changing what's used in the Eucharist.

TLDR: Some people think that alcohol is permissible in situations when other water purification technology is unavailable. There are historical and theological reasons and I went into them a bit.

If requested, I will try to find sources later. On phone now and that is difficult for sourcing.