I believe the most effective way for government to protect Individual Rights is for it to be limited in size and reach, open in its processes and proceedings and accountable to those it serves.
Government must be limited in size almost exclusively due to cost. A large bureaucracy is more expensive than a small one, and funding for government activity comes primarily from tax payer money. The larger government is, the higher its tax rates and the less ability individuals have to pursue Happiness. Government reach must also be limited so as to prevent unnecessary regulations on individual Liberty. The idea of limited government reach can be found in the Tenth Amendment to the United States Constitution.
Government must be open to ensure Rights are protected, not Privileges. When a government conducts its actions in secret, the temptation of elected officials to grant Privilege to themselves and their friends is unnecessarily high. Crooked deals, unethical agreements and special treatment are far more difficult to achieve when the People have access to records and proceedings. Freedom of information legislation has done a great deal to ensure open government. Similarly, laws that prohibit or punish the actions of the people must be published and readily available. Secret laws are impossible to follow and impossible to protect against, a huge detriment to Liberty.
Finally, government must be accountable to the governed. If a government has not met its responsibility of effectively protecting individual rights, the governed must be able to hold their elected officials accountable, either by removal from office or by trial. For a government to be unaccountable, for its actions to be unstoppable, for its decisions to be unquestionable… that government is no longer representative or capable of protecting rights – in fact it is “destructive of these ends”. It then becomes the People's “right, it is their duty, to throw off such Government, and to provide new Guards for their future security.”