There's a fair amount of hindsight bias going on with this critique of phlogiston. Phlogiston sounds plausible on the surface. It's a reasonable conjecture to make given the knowledge at the time and certainly worth investigation. Is it really any less absurd to postulate some mystery substance in the air that essentially plays the same role? If they'd chosen the latter, we'd be lauding them for their foresight.

It's perfectly feasible to draw up tables of the presumed phlogiston content of various materials and use this to deduce the mass of the residue after complete combustion. You could even predict how much of a material would burn if placed in a closed container. Phlogiston or oxygen, you get the same tables and the same empirical laws--before anyone discovered the latter. It's a lot easier to come up with empirical laws than it is to explain the underlying mechanism.

Is anyone satisfied with a physical theory content to give empirical laws and which makes no comment on underlying mechanisms? Gravity was used because it worked, but I doubt anyone was comfortable with the action at a distance. The Copenhagen Interpretation is an active refusal to engage in any kind of speculation as to why quantum mechanics "really" works, and routinely gets slammed on this site.