I like to think that the dusty stuff is beneficial not just for your Tomato plants, but also for the aquatic kind. Therefore, I have stopped washing Flourite when setting up new tanks.
After adding the substrate, but before filling the new tank, I siphon out as much water as I can, which moves the majority of dust stuff into the lower layers of the substrate.
Then I fill the tank very, very slowly, over a couple of hours. Not good for the impatient type, but keeps the dust for plant roots, and gets you a clear start anyway.
There is an initial time where stuff collects on the surface, but again, after a few weeks of skimming that goes away all by itself.
Just offering a different opinion, a different way of doing things.