I don't see why not.
Yes, some CO2 will be lost from the surface agitation, but you simply up the injection (I think the difference is negligible). In fact for tanks with very little surface agitation there is a risk of CO2 build up even if you turn off CO2 at night. Some folks run air stone at night to disperse CO2 for the sake of the fishes, I've tried this and it works.
I think running air filters will provide good surface agitation, and once you've tuned the CO2 injection rate to your optimum level during photo period, you can get good CO2 and O2 level in the tank. O2 and CO2 are not mutually exclusive, which means you can have more of both at the same time. In fact I will aim for that, its good for plants and faunas.
Since you're using air filters, you should ponder about is how to dissolve the CO2 efficiently and distribute it to the plants.
CO2 is cheap, don't worry about it. Small price to pay for a nice tank with good plant growth and happy fishes.
Disclaimer: I've never run air filters before.
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