What is difference between funding an MS and a PHD student I am trying to understand this regarding aspects of funding only and not quality of research.What is difference between funding an PHD and an MS student. 

I thought both took courses, get some stipend and advisor funds them.Maybe for PHD they fund students for 5 years instead of 2 years of MS ? 

Is there any other major difference?

I understand PHD student's research output expectations are completely different.I am asking this question with specific regards to state universities in US.
Disclaimer: this is US-specific and quite likely engineering specific. 

The only potential difference is that the rates for funding Ph.D students (post-candidacy) might be different to that of an MS student. But the difference is usually between types of funding(RAship, TAship, etc), not who gets funded.