You'll hear it from any relationship counselor: Communication is key. Indeed, open and clear communication will help in almost all personal and professional relationships, and the coach-parent relationship is no exception.
Countless coaching guides recommend having a parents meeting at the very beginning of the season, or even better, during the preseason. At the meeting, explain the details of what will be expected of the players and parents. Most importantly, take this opportunity to explain your coaching philosophy -- emphasizing your intentions to give every player a fair shot and your rules about playing time (if it depends on practice attendance, for example).
Also, be sure to explain your rules regarding parental involvement. This might include asking parents not to shout directions to their child during the game. Let them know that if they have a suggestion or notice a problem, they are free to come up in private to discuss it with you. Confrontations in front of the players are never a good idea. Encourage parents to attend practice if they want to. This should help you reach the goal of open communication and help parents better understand decisions you make on game day.
You need to encourage positive behavior from the parents, so that they can in turn encourage the players. Tell the parents that you can't have them negatively yelling at referees or at players. Or, if you don't ask parents outright to be positive, then at least express it by example. Stay positive and express that you're excited to be coaching their kids.
The parents meeting will not only give you a sense of what kinds of parents you're dealing with, but it will give you a chance to establish a good relationship with parents. The best way to do this is to make sure to open the floor for parents' questions.
If assembling a meeting isn't feasible, consider compiling a handbook, or at least write a letter to parents that addresses all these issues.
Although this open communication helps, it might not be enough to prevent meddlesome parents. So, let's get into the nitty gritty of how to deal with particular kinds of helicopter parents.