I don't use Endnote, but I frequently edit Word documents whose bibliographies have been prepared using it. The following contains much extrapolation from personal impressions.
They have different ideas about use. Endnote is a bit more like Zotero than traditional Bibtex, stressing its access to official abstract and bibliography servers, with many users who have never either edited a bibliography entry themselves, or felt that they are maintainers of a bibliographic database, because they haven't felt the need. The idea is that that the professionals have taken care of the massive Endnote bibliographic database, so that you don't have to worry about it. This idea of being taken care of is supported by the work that the Endnote producers (recently Endnote was acquired by Thomson-Reuters, now one of the world's two giant news & professional information agencies) have put into cultivating a dialog with the major style guides, such as APA, so that their output is accepted by the authority as being in conformance with the official style.
The results are pretty good, but not as good as users expect. Very commonly I received manuscripts from clients who say I don't need to look at the bibliography because it was prepared with Endnote. I then look over the bibliography to see if I find any errors. Inevitably I do, occasionally serious ones, which I report back to the sometimes very surprised client.
Endnote allows export to Bibtex format. If you do so, the promises about conformance to style guides become worthless, as the Endnote representation of reference metadata does not cleanly correspond to Bibtex's. I have the idea that the same problems will apply if one tries to convert Endnote's format into the new Word 2010 reference format, but I have not confirmed this.
Bibtex is free. The standard Endnote package has an RRP of $300, and will require fairly frequent paid upgrades for most of its users.