Loop counters really are not the problem. The problem is that even when using unsigned integers you often want to do 'signed math' on them (e.g. adding a negative amount, or you could have an expression made entirely of unsigned integers (like ((x - y) + z) where an intermediate result may become negative even when the end result is positive - and in languages with overflow check that may result in a panic).

A better rule of thumb is to always use signed integers, except for bit twiddling and modulo-math.

Especially with 64-bit integers it's really no longer an issue to lose one bit for the sign (63 bits ought to be enough for anybody heh).