Why is protected water usually safer than unprotected water from wells or rivers?

Protected water sources are the ones that are protected from contamination or pollution. Generally, water bodies that are open to environment and close to civilization are prone to contamination by environmental and human interventions. The typical contaminants found in such unprotected water bodies include solids, colors, chemicals, odor, etc. The presence of such contaminants makes the water unfit for human consumption unless it receives appropriate treatment. 

Water bodies that are deep underground or from sources such as glacier are typically uncontaminated and, hence, are safer for human consumption compared to the unprotected water sources. 

Water source protection is thus necessary, especially in developing and underdeveloped countries, where lack of uncontaminated water causes diseases and aesthetic issues. An example of water source protection is providing lining to a well and keeping it covered.

Hope this helps.