Keeping this purely to custom and tradition rather than religion as such...

It's based upon something that St Paul wrote in I Corinthians and at the time culturally it must have been considered a distraction. Head covering didn't require a hat, which were a later development in any case, but today a hat is considered as a head covering.

For some reason the wearing of male headgear in a church became limited to the clergy - mitres, birettas etc. in both eastern and western traditions and therefore the male laity were expected to remove any headgear upon entering.

There were some groupings that allowed male hats - the Puritans and the Quakers wore them for example but that declined with time also. It's only fairly recently when headgear for ladies was seen as optional in many traditions.

When it comes to highland wear it would still be the tradition to remove head coverings, even if piping, before entry and that is certainly the practice in the UK armed forces for all uniformed personnel to remove hats even when a Church Parade is held in the open air.

It's less an issue of fairness than respect.