Is it plausible that a planet can be breathable despite the color of it's atmosphere? My story takes place in an alternate reality in which what people thought the Solar System was like in the 50s, Venus is a swampy, breathable world, Mars is a dying, desert world with canals, but it is breathable as well, is the reality. Would being breathable affect it's atmospheric color or should I just not bother?
There are several factors that come into play:
Raleigh scattering. The peak scattering depends on the air pressure. Lower pressure = larger average distances between molecules = redder skies, all though in fact you would need a very deep low pressure atmosphere (large low density planet) to get much visible reddening.
Dust in the air. Again size will make a difference, as well as the colour of the dust itself. If the dust is transparent to some colours, and reflective to others you could get some wild looking skies. Look toward the sun, and transmission colours dominate. Look away from the sun, and reflective colours dominate. Very small dust/fog particles preferentially scatter blue light, hence the blue distance haze over forested lands. Thin enough flakes of gold transmit green light.
Amount of atmosphere above you. As you climb and have less air above you, you get less blue scattering. Net effect is that the sky is darker blue. Also since more of the light is only scattered once, there are directional effects to sky colour. The converse should be true, but I've not tested it -- as you get lower you should get more scattering, and get fainter blue. While I've seen this, I've ascribed it to just more dust and water droplets in the air.
Gasses with colour: Chlorine is a yellowish color. One of oxides of nitrogen NO2, I think, is reddish brown. Red fuming nitric acid (RFNA) is NO2 dissolved under pressure into nitric acid. Used to be used as an oxidiser in liquid rockets. Evil stuff. The fumes turn to nitric acid in your lungs.)
I think all of them are bad news.
The atmosphere is clear because evolution has made our eyes good at seeing through the atmosphere. Our eyes are able to detect the visible spectrum of light mainly because the atmosphere around us has a hard time blocking these wavelengths and it was advantageous for us viewing it. There are definitely wavelengths where our atmosphere would be rather opaque. Color to us us just a way of differentiating wavelengths of light we can already detect with our eyes. So it is unlikely native species that breath the atmosphere would ever see color in their atmosphere, they would have evolved to see the wavelengths that are able to penetrate their atmosphere.
Although there are few natural gasses that are breathable for humans and are very colorful, it doesn't really mean that color in the atmosphere is can't be dyed with something completely harmless. The process that makes the color can be completely natural like pollen or other airborne organic molecules released by other life forms. The only problem with airborne particle as a cause for coloration of the atmosphere is that it might be breathable for a while but humans probably can't deal with density of gunk in the air and the material will probably get into the lungs and kill you slowly.