A transaction can contain multiple inputs. You could have a transaction that combined many of these tiny utxos and the total input would be far greater than the fees.
You can’t stop markets when there’s open competition for scarce resources which have alternative uses. In this case, it’s putting data into a globally distributed database. Other than a fee market, how else do you expect to regulate write access? One alternative to somehow lowering fees is to just use thebitcoin blockchain as a settlement layer, i.e. use lightning network or something.