Most oil filters remove particles as small as 25 microns (about 1/1000th of an inch) -- but there are particles circulating in your car's oil that are even smaller -- particles that even the newest, best filter can't keep out of the system. And even tiny little bits like that can cause wear over time. They can also band together to create sludge and deposits.
If these particles become excessive, clean oil alone can't flush them out. But the chemicals used in an engine flush can -- stopping any further wear and giving the new oil a chance to do its job properly.