For the most part, it is merely because chameleons are so different to most mammals. They have evolved a number of curious and almost fantastical abilities.
The fact that they are able to change colour. Their almost 360 degree stereo vision due to their bulging, swiveling eyes. Their long tongues that strike with pinpoint accuracy. These are all abilities that are almost alien to us: indeed, skills like that are often the subject of science fiction stories.
So all of these weird traits tend to unsettle us. Particularly if people have little knowledge of biology or science in general, they can be quite disturbed by a creature so different to ourselves.
Add to that the fact that chameleons are reptiles, a group of animals for which humans have historically had a distaste, and you start to see why some people fear them. Green chameleons dwell in the trees in southern Africa, along with their reptilian cousins, the boomslang and the green mamba - snakes which are very much feared in these regions. It's easy to see how some of that fear is transferred to the chameleon by association.
In most African mythology, the chameleon is regarded as a creature of distrust and deceit. This is linked to its colour-changing ability. A leopard never changes its spots, but chameleons can turn any shade of the rainbow - hence you can't trust them.
Even in the English language, the term chameleon is used to refer to someone who is changeable or fickle.
The Zulu people have a story of how the slow chameleon failed to deliver God's message of immortality to humans, and instead the message of death reached mankind first, and that is why humans remain mortal.
Check out the following links:
The Feared One
Unwaba
In essence, it all boils down to a lack of understanding about these beautiful and fascinating creatures.
And it's not only a fear that exists within primitive cultures: even my mom has a strong dislike of chameleons' scaly, reptile skins. She never goes near mine!
