Freedom to maintain opinions about religion without such opinions affecting civil capacity. Again I will bring up the fact that prohibiting government sponsorship or endorsement of religion translates in the most freedom to exercise religious practices. Even allowing prayer in school imposes some restrictions on those who do not pray, do not pray to the same God, or believe that public prayer is sinful. By allowing that seemingly harmless practice you may be severely curtailing religious liberty. By saying there will be no prayer in public school which is organized and presented to the entire class at a certain time every day, you are in no way limiting any one's freedom to practice or worship their religion.
Children can still say a prayer to themselves to start the day.
They can say grace over lunch. Talk to their friends during recess about what they did at church or an upcoming religious holiday or celebration. The secular goal is to be able to educate the public as much as possible so that acquiring jobs, participating in the political process, fulfilling individual potential becomes possible. Financial support of religious schools through vouchers means that taxpayers who disagree with a particular religious doctrine, history or philosophy would be forced to financially support its perpetuation. By prohibiting financial support through vouchers, religious liberty has not been compromised.