Modern ones "skim" along the terrain, this massively reduces their radar detection range (due to the horizon) and allows them to navigate around known defensive measures.
This is also why both the US and Russia has spent millions of dollars on extremely sensitive microphones to literally "hear" an incoming cruise missile.
A system like this, combined with a system to combat high altitude cruise missile attacks, could theoretically work. Or certainly limit/disrupt the ability for very low altitude weapons to enter your territory uncontested.
Plus low altitude drones definitely have a future, particularly against a technologically advanced nation.