I personally just don't see the rationale of those who think that God doesn't want them to play instruments in church

Actually instrumental Christian worship is pretty new, as Christianity goes. John Calvin (d. 1564) considered instruments in worship anathema. Martin Luther (d. 1546) considered the organ an "instrument of Baal." Lutherans didn't begin using instruments in worship until he had been dead 100 years. Charles Wesley (d. 1788) said, "I have no objection to instruments of music in our chapels, provided they are neither heard nor seen." The Catholics came this close to condemning instruments in worship at the Council of Trent (1545 ff) -- which would have sealed it permanently.

The real question is why and how they came to be accepted, rather than why they are still rejected in some places. It is the accepting, not the rejecting, of musical instruments in Christian worship that is the novelty.