I don't think what you're saying makes sense.
Take Washington state for example.
According to this, I think the average sales tax rate is 8.2%. http://www.dol.wa.gov/vehicleregistration/ftrefunds.html
So, if an out-of-state retailer, which has no nexus within Washington state, were to pay sales tax, instead of having to figure out which locale to base the sales tax on, then keep it in their records what amount was collected goes to where, they'd just collect 8.2% under a special code in my idea.
Then we'd look at statistics. Based on non-online sales, we'd look at the total gross receipts. We'd also look at the gross receipts for all the locales. Let's say a given taxing locale is responsible for 0.31% of all the gross receipts. Then that locale would get 0.31% of the revenue collected under this special code. The algorithm may be readjusted if it turns out some locales tend to do way more online purchases than others, possibly due to remoteness.
But yes, some people may be paying more in sales tax than if the online retailer were to collect based on their taxing locale. But unless someone is making large purchases, I can't imagine it being more than a hand full of dollars per year. I mean, if someone is "overpaying" in taxes 1% per year, and that person only spends $1k per year on online purchases from out-of-state businesses, that'd be $10 more per year.
Another option would be instead of having the sales tax rate based on the average sales tax rate, it could be based on the lowest sales tax rate in the state, which, in Washington state, would probably end up being 7.0%. Although, that still would be restricted to out-of-state businesses which have no nexus within the state. While it still wouldn't equalize things with brick and mortar stores, it would bring them closer.