What alternatives did you consider?
That said, this isn't a buy and bury situation. Mendeley is now very well positioned to dominate so there's no reason to worry, and anyways you can always take your data with you.
FYI - I work for Mendeley.
While I don't know the specific details of your agreement with Elsevier that make you so "well positioned to dominate," I do know that your target market's principles are more closely aligned with ours than with yours, and that they aren't stupid. You can't really preach open access for years and then sell yourself to the OA movement's greatest enemy and expect that no one will notice.
In any case, I welcome the competition, although I hope that in the future it comes in the form of shipped code and not more lies about the viability of free software.
FYI - I'm a member of the Zotero core team, but I'm also a graduate student in neuroscience at MIT.
In an ideal world, everyone would pool their resources toward free software and all would benefit. In reality, it is like a multiplayer Prisoners' Dilemma: people who "defect" by using proprietary software are rewarded (in the short term) with a nicer UX, at the expense of those who "cooperate", and at their own long-term expense.
There are other problems: FOSS (especially Linux) suffers from severe fragmentation, and I also question to what extent people are willing to develop software that is not fun for free.
Anyway, I never "forgot" the excesses of, say, Y2K-era Microsoft. I have just been skeptical of the workability of FOSS. But I do think it is the ethical way to go.
Pay them to develop the features you want rather than pay the cost of using proprietary software or closed systems.
Everyone wins.
I don't blame the Mendeley team -- too much -- since $100M is a lot of money. Although they shouldn't try to pretend that this isn't a complete sellout.
The fault really lies in the community's willingness to fall over and over for these shiny but not-quite-free alternatives. Two years ago, I would have said that Stallman is a nut; now, I think he's quite right.