The simplest answer is that humans overwhelmingly rely on their eyes as their main sense organs. So when someone has a tattoo on a part of their body that is visible, they will inevitably be treated slightly differently (on a subconscious level) than someone who does not.

It will depend a lot on the culture and the beliefs of the individual whether tattoos are seen as positive, neutral, or negative. For instance, in tribal/aboriginal cultures, tattoos often serve a spiritual purpose and will be seen positively by that culture. In others, it is more neutral or will depend on the individual's views.

In still other cultures, it will be viewed in a negative light for various reasons. I won't cover all the reasons for viewing tattoos negatively in this answer as it's a bit beyond the scope of this question. Some reasons could be: 

1)Tattoos can be seen as a form of self-harm/self-abuse by some.

2)Getting tattoos may go against one's spiritual beliefs because it is viewed as desecrating something sacred (the human body) which is already perfect.

3)People may have stereotypes that people with tattoos are more likely to be users of drugs, criminals, mentally unstable, and/or engage in other high-risk activities.

Some of this is based in reality, and some is based in ignorance: but let's remember, the main reason people with tattoos are treated differently is that they look different, which is the most important sensory data the brain uses to categorize and collate information about the physical world. To emerge from this prejudice requires significant mental effort for many. It's important that we treat all human beings with love and respect, regardless of what they look like, but that doesn't mean it is effortless to do so.