There is nothing wrong with using any of the pay sites as sources. You must remember these are not actually sources, but only repositories. It is no different than me telling you what library I found a book in. While there may be some frustration in not being able to click on a link that doesn’t make the reference any less valid.
There is a big difference between ancestry.com, heritage.com and AmericanAncestors.org.
The primary problem with ancestry.com and heritage.com is not the websites but the quality of the sources. They are often just people’s individual family trees and are filled with errors. Because they are behind a paywall it is often difficult to be able to assess the quality and accuracy of the data. In the case where actual documents are referenced to on ancestry.com, I see no problem with this at all. The main point people make is that many of these documents are available for free at FamilySearch.org, so it is preferable that if you are going to provide a link that it be to the free site.
AmericaAncestors.org provides access to high quality, peer reviewed journal articles. They provide access to a wealth of original primary documents not available elsewhere. The sources are these documents, not AmericanAncestors.org. It is just a courtesy and a convenience if I provide the link to where the documents can be found. While it is certainly preferable to provide a link to a free site, much of what AmericanAncestors.org provides is not available anywhere else.