I had a family member who worked for Nielson for years. And I work in the cable settop industry.
Nielson can put modules in cable boxes. In those boxes, depending on the cable company and hardware provider, they can also install applications for those settops that require users to enter codes indicating who's watching the tv. So if you change the channel - you're prompted to enter a code indicating if you're the mom, dad, kid1, kid2, whatever.
That data can either be fed to the neilson hub... or depending on the cable system/cable provider, can be sent upstream to the cable operator's "head end"... and then transmitted to Nielson.
Only Nielson households have this extra module and/or extra application in their settop box.
Nielson does not do a good job capturing data on dvr use in non settop boxes (roku, tivo, etc.) But I believe tivo does it's own viewership monitoring... for the household. (Not per user.) Cable operators also have the ability to gather household viewership monitoring. (capture what channel is being tuned, when, etc.)