Because a site is a permanent record of a real place, and survey responses attach to it. That is what lets you ask how one water point has changed over five years, rather than only how a district looked on the day you surveyed it.
Video: The Power of Sites in mWater on YouTube
This is the single design decision that separates a monitoring system from a pile of surveys. Responses that stand alone can be counted but not followed, so every round of data collection starts over and nothing can be held accountable for a facility over time. Sites also make data shareable: because the facility exists as its own record, a second organisation can add its own monitoring to the same place instead of creating a duplicate.