Stupid Banking Question

If I make more than 6 on-line transfers in a month from my savings account to my checking account, I get charged a $9.00 fee per transfer after the first 6 and there's a possibility that my savings account could be converted into a checking account. However, if I make more than 6 withdrawals from my savings account at an ATM or using a teller and deposit those withdrawals into my checking account at an ATM or using a teller, then nothing happens.

They say this is because of federal regulation D.

I don't understand the logic here, that I get charged a fee for doing it one way, but I don't for doing the same thing another way?