James Whitman argues that they are the result of historical developments in the late 18th century which are now applied to a role for which they were not intended.
His thesis is that the "beyond reasonable doubt" standard was originally constructed to protect jurors, not the accused. Specifically, it was protect Christian jurors from eternal damnation for falsely convicting an innocent person, particularly in capital cases.
Theologically, if a juror had doubts, the only way to avoid sin was not to act i.e. to acquit. Indeed John Adams was explicit about this in his (successful) defence during the Boston Massacre trial. The rule was therefore introduced to make it easier for a jury to convict - exactly the opposite of the way it is used today.
In civil cases, where the accused's life or liberty was not at stake, such a rule was not needed; a juror could have any number of doubts and still go with the more convincing argument without imperilling his (they were always men) immortal soul.
As theological interpretation has changed and a more pragmatic and secular view of the law has arisen over the last 2 and a half centuries, the meaning has changed and is now seen as a way to protect the accused where their life and liberty are at stake in a criminal trial.