I don't agree. If you play up the Woobie-esque nature of being a parasitic organism, it can work just fine. Treat the entire race as more of a handicapped existence (you might need to ignore Unfortunate Implications by comparing them to the poor, the sick or the elderly just to make your point) and then at the end, establish that this is all by choice.
@Mammalsauce:It's not so much "They're evil" as "They're evil and they don't intend to stop. Ever."
I'm feeling strangely happy now, contented and serene. Oh don't you see, finally I'll be, somewhere that's green...If I understand your idea correctly, the parasites are not normally intelligent. They have to take over a human host before they can do anything but eat and excrete. And (as usual) you can't remove the parasite without killing the host.
And the catch is that, once they have a host, they scheme to get more hosts. In other words, they try to propagate their own species. Is that evil or just instinctual? True, they lie about the artificial host thing, but if they told the truth, humans would wipe them out. They don't have to be completely evil, just dangerous and alien and liars.
Don't forget, the whole "Puppet Masters"/"Invasion of the Body Snatchers" meme took hold during the Red Scare. Anyone could be a Communist. Anyone!
Under World. It rocks!Interesting premise.
I wonder if they would still seem sympathetic after the revelation. If taking over intelligent beings is their only way to survive then they are offered a choice between evil and death, which isn't a situation anyone wants to be in.
If they use the host's intelligence do they also pick up elements of the host's personality? Do they have access to the host's memories?

The antagonist in my story is basically an alien race where everyone is a Puppeteer Parasite. Everyone respects them (with a few exceptions), despite the fact that their very existence requires what basically ammounts to the death of humans, under a combined pretense of "a)They need to do it to survive," and "b)They're working on constructing an artificial unintelligent kind of host". The twist at the end that establishes them as more evil than they previously seemed is that they're NOT actually putting any research into artificial unintelligent hosts, because their intelligence derives from their host's intelligence, so by definition they cannot create an unintelligent host and remain an intelligent race.
Does this sound like a well-thought out, rounded antagonist?
I'm feeling strangely happy now, contented and serene. Oh don't you see, finally I'll be, somewhere that's green...