I run a few leagues myself and have run into this. How I do it is if it's a major change to the league (like how many we keep, stats, postions etc), I do not change the rules regardless of how many people vote for it. I run an established league and if a new teams wants to change something major, then he/she can leave the league and join another league.
Small rule changes I don't have a problem voting on.
What I have learned is that not everyone will be happy with a particular league setting. And you can't please everyone. If you change a rule every time someone wants to vote on it, your league will turn into something that you as the commish will not like.
I look at it as it's MY league, I do all the work in setting it up, finding replacement teams, keeping everyone active to maintain an active league and so on. I started commissioning leagues because I was tired of leagues that I was in not being ran properly and always had these rule changes that made it less fun for me.
So far it's working for me, in my 12 team league, had all original 12 teams return and in my 16 team league, only had to replace 2 people. I'm doing something right.