I think this is another preference question with no correct answer. Though for me the advantages of having one big tree seem so clear and that's how I have always done it.
If it is important for you to be able to export GEDCOM files that are limited to one line of your ancestry then you probably prefer separate trees. Maybe there is some other reason that makes it important for you to compartmentalize your data.
I have a single tree on Ancestry.com, approaching 4,000 persons, that includes all the people I have researched via Ancestry. Some of them are disconnected from the others because I haven't yet found enough information to link them into known lines. I have not found any disadvantages of this approach.
In my LifeLines database, which is decades older, I have about 16,000 person records. A good number of these are what are sometimes called "persona" records, so the database probably has about 14,000 "conclusion persons." Again I have only one single database for all my data.
If I were a professionaly genealogist, I would have a tree for each client. And when I do work for friends I keep their trees separate. But for my own tree, which is also combined with my wife's ancestry, as well as the ancestry of my sons-in-law and daughter-in-law, since they are ancestors of my grandchildren, it all goes into one big tree.
In addition, my single tree is also growing into a one-name database for the Wetmore surname. There are no disadvantages that I have ever felt for keeping all this data in a single "tree." I put tree in quotes here because obviously this isn't a simple tree. I basically go whereever the data goes.
On the Ancestry.com side, when you export GEDCOM, I'm not sure if you can limit the sections of your tree that are exported. However, with LifeLines I can fine tune exactly what part of the database I want exported. This way it is trivial to create and send a custom GEDCOM file with a precise subset of the overall database. If I want to send a subset of the Ancestry.com database, it is easy to export the whole thing as one GEDCOM file, import that GEDCOM file into a fresh LifeLines database, and then use LifeLines to "re-export" the precise part of the entire tree that I need.