Well there is only two of those that pay for everything basically; LAG and LAFC. However, nothing is completely free as transportation and time costs factor in not to mention there are certain obligations and/or community events that players need to participate in.
For other Non-MLS organizations, there can be dues or partially things that parents have to pay for like mentioned (some have uniform fees) but typically there is 3k+ or more of travel of expense, Winter Fest, Playoffs, Cups not to mention others tournaments. Yes there are fundraisers that can help with this but that's team based or maybe one favorite team within a club gets covered. These type of clubs have poker night, golf tournament, and other various fund raisers they want parents to participate in.