I assume that you're talking about the backcountry, but one of the primary reasons for a boil order is when sewage infiltrates (or may have infiltrated) the municipal water supply. That sewage can contain all manner of viruses that you wouldn't normally find out in the bush, like hepatitis, say. Whatever diseases humans can pass through the oral-fecal route is fair game.

Plus, a boil order needs to take all segments of the population in mind, such as infants, the elderly, and people with various conditions who have greatly weakened immune systems.

So, a filter may be fine in most cases for a heathly adult to use on a hiking trip, but that's not necessarily an equivalent situation as a boil order back in town. If you have any of these vulnerable segments of the population in your care, then it makes sense to boil.