1. A method of operation of a navigation system comprising: generating a signal weight with a control unit based on a feature extracted from a user activity; generating an activity model based on the signal weight for representing the feature as a positive weight or a negative weight depending on an activity type, a category of interest, or a combination thereof; classifying a user entry based on comparing the feature of the user entry to the feature represented in the activity model; and determining a user's intention based on the user entry classified for presenting a point of interest on a device.