Yep. That's to be expected if you want shoes that breathe. I'm on my third pair of Hardrocks.

If I'm doing a very long day on dusty trails I'll stop around halfway, rinse off my feet, and don clean socks.

Waterproof shoes with a Goretex liner will keep the dust out but your feet will sweat too.
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If you only travel on sunny days you will never reach your destination.*

* May not apply at certain latitudes in Canada and elsewhere.