One thing readers should understand about this question (which should probably be added to the question text, hint, hint) is that lightning happens when highly charged air in the atmosphere finds a good enough conductor to the ground in order to arc there. Thus it is naturally attracted to tall pointy things. This quite well describes the steeples (or crosses) atop many churches. In other words, due to some unique properties of their most popular architechtural styles, ironicly lightning does happen to be attracted to Christian churches.
This of course did not go unnoticed in the Age of Enlightenment, and was a source of much theological angst.
Before Benjamin Franklin proved the relationship between lightning and electricity, and (arguably) invented the lightning rod, it was already observed that churches were more likely than other structures to get hit. For example Peter Ahlwardts suggested avoiding churches in lightning storms in his "Reasonable and Theological Considerations about Thunder and Lightning" written in 1745.
It does appear that there was a large segment of religous thought that prayer, with a generous helping of religous-like activity, should be sufficient to protect churches. Sadly, a lot of this activity involved church bell-ringing. Bells being metal, and operated from high in the church tower, this had an unfortuate toll (pardon the pun) on the poor bell-ringers.
The paper I linked above does indeed claim that the newfangled lightning rods were viewed as thwarting God's will (lightning strikes) and were sometimes even torn down by mobs. Supposedly the Reverend Thomas Prince even went so far as to blame Franklin's lighning rods for causing earthquakes. The principle there being (I'm guessing) that God now had to find ways other than lighning to show his displeasure.
Franklin went so far as to write the following to the President of Harvard:
How astonishing is the force of prejudice even in an age of so much
knowledge and free inquiry. It is amazing to me, that after the full
demonstration you have given, that they should even think of
repairing that steeple without such conductors.
Eventually of course people got used to the things, and practicality won out over other considerations. For instance, according to my linked article:
A typical case was that of the tower of St. Mark's in Italy. In spite
of the angel at its summit and the bells consecrated to ward off the
devils and witches in the air, and the holy relics in the church
below, and the processions in the adjacent square, the tower was
frequently injured and even ruined by lightning. It was not until
1766, fourteen years after Franklin's discovery, that a lightning rod
was placed upon it, and the tower has never been struck since.