A standard justification for any unusual character to maintain a Masquerade, because The Government is Evil and Science Is Bad and if the authorities got their hands on them, they'd stick them in a concrete box and perform all sorts of cruel experiments to find out what makes them and/or their special powers tick, either destroying their quality of life, or killing them outright in hopes of getting all sorts of goodies.
Scientists will usually be portrayed as too obsessed to care for anyone or anything who might be used to further our knowledge of the universe or make a cool new weapon, caring only about the fame or payment they'll receive from their higher-ups. Only one bad scientist is enough to spoil your day, but in settings that use this trope the majority of encountered research workers are likely to be like this.
The oddest part of this trope is that the danger may never even materialize within the story — but the certainty of it happening will never be questioned by anyone concerned. Humans Are Bastards after all, Inhumanable Alien Rights be damned. All the more reason to keep up their disguise and lay low, or else they may get captured and taken away.
Sadly, there is a lot of Truth in Television to this trope. There is a long and dark history of human subject researchand the early days of biological science didn't have the advantages of modern noninvasive tests or imaging. Often, the only way to make advances that would potentially save uncounted lives was to experiment, a dilemma that science has struggled with for centuries. Protections such as ethics committees and anti-cruelty standards were created by scientists specifically to prevent the bad apples from carrying out these abuses, but it has been a long evolution, much like abolition or emancipation.
Modern research works a lot less intrusively as sonography, MRIs, and other medical imaging techniques have made hands-on vivisection less necessary for the internal examination of research subjects, and laparoscopy and microscopic biopsy give both more useful and more humane methods of seeing how things work in living subjects. Given sufficient funding and resources, there should be no reason for slicing off a limb just to see how it looks on the inside. The Playing with Syringes mentality of fictional "research" also happily ignores the fact that when you only have one specimen, it is a good idea to take care of it because once it stops working it'll be much harder to figure out how it used to. Of course, being locked up is cold comfort to the specimen — it just means the torture will be of a greater duration, and would still result in them being locked away somewhere against their will. Just because they aren't cutting you up doesn't mean they ever intend to let you wander off (or that you won't wish they were). However, the Only Sane Man might point out that, if the subject is intelligent and capable of speech, they can save a lot of time and effort by getting his compliance, or even simply asking him questions about their powers/anatomy/biology (allowing them to get more clear answers and not have to go through the trouble of restraints or a manhunt).
Then there's the question of medical ethics. In Real Life, medical researchers have to follow very strict testing standards to be able to publish their results. Getting caught violating them can easily end their careers and leave them facing civil or even criminal charges. Of course, these considerations only apply to scientists who intend their results to be publicly documented. It can be expected that various black ops organizations that either suspect or already know about the Masquerade won't care at all about any of this. (And crime is only punishable if one is caught.) Further, who knows what organizations like these would do with the knowledge they gain. So, you'll probably want to do your best not to get caught by them just the same.
For obvious reasons, this trope is often Played for Horror. If the scientists get what they want, Body Horror may follow. Expect to see Mad Scientist, Evilutionary Biologist, and possibly Men In Black as well.
Compare Alien Autopsy, in which the fantastic creature being studied is usually dead when human scientists find it in the first place, which would make such an up close and personal study sound significantly less unethical; Medicate the Medium, in which the special ability would be dismissed as psychosis and treated as such; Playing with Syringes, in which unusual characters are the result of experiments, rather than being experimented on for being unusual; and Superhuman Trafficking, which is a general trope for the exploitation of unusual individuals. Organ Theft may occur as a result of this trope.
