Bad first impressions combined with ignorance.

A person is playing his character in a contested zone or a battleground. He gets steamrolled by five characters that seem suspiciously like they're being run by a bot. His anger at being so casually one-shot is made worse by his belief that the person who did it is cheating. When he learns about multiboxing, he already has a very negative view of it, and is unlikely to consider the issue rationally.

Or...

A person is playing his character on a PVE server and watches as a group of characters that look suspiciously like bots run around nuking everything in sight. His first impression is that it's a gold farmer who is botting characters to grind gold or items. When he learns about multiboxing... see above.

I would guess that most people are very inflexible in how they reason these things out. They follow their first impression and often refuse to change, perhaps out of stubbornness, or pride, or just flat out stupidity. If you've ever followed the debates on the forums, you will notice that a good number of people use an argument like "I don't care what you say, it's cheating (or automation) and it's wrong." In other words, they made up their mind and they're not about to let things like logic and knowledge get in the way. That, to me, is the sign of someone who is upset over something that happened and has let that experience color their point of view without even trying to understand or be reasonable.

So the short answer is: People are stupid.