It exists because some states are very sparsely populated while others actively suppress the votes of a large portion of its population, first by slavery, then by other methods. It's fair to increase representation of underpopulated states because their interests would be underrepresented if not (and it's a good thing because it allows large areas to be dedicated to nature).

Unfortunately, there is no mechanism in place that actively punishes voter suppression. Voters per inhabitant ratio and election turnout could be used to penalize states with low engagement to ensure voter suppression does not occur.