At issue is who scanned the material and when and then who indexed it. The four sites are http://www.Familysearch.org – free, http://www.HeritageQuestonline.com – library based, http://www.Footnote.com – subscription, and the 800 lb gorilla – http://www.Ancestry.com – also subscription based.
Over the years I’ve found that the best quality census records came from Heritage Quest. They also have the best search capabilities for census information. I finally found a missing ancestor by searching for the given name and country of birth instead of searching for the surname. Heritage Quest brings up a list of results by state and finding my ancestor was much easier.
Ancestry.com has upgraded their images recently and FamilySearch.org has wonderful tools for showing other names on a page with links to images which may include Footnote.com. Footnote.com has very high quality images and good tools for inverting from black on white to white on black at high quality.
The other thing if found out about census records is that not all holders of these census records have indexed all years and all people and all states! Don’t just assume that the site has done this work. Check the “about this database” or "What's new" notes before you enter a search. You may be looking for information on a site that they have not even indexed, yet. Heritage Quest recently completed indexing the 1930 census but recently they only had Connecticut, Delaware, Maryland, Texas, and Virginia indexed and online. No wonder I could not find my Pennslyvania ancestors there in 1930.
So your ancestor may be hiding on another website’s index.