Oooookayyyyy....
1) The ships in ED are not actually propelled by a chemical reaction. The fuel is used to power a space compressor that creates "waves" in the space/time continuum. Your spacecraft doesn't move actively, it "rides" those waves and is pulled and pushed forward by them just like a surfer. (I am not joking here. This is a physically possible mechanism, discussed for spacecrafts in a far future!)
2) There is a (again: real!) theory that, should you ever be able to fly close to the speed of light, you would be able to experience a quite surprising effect in the surrounding space. All of a sudden, space would start to "boil" and all sorts of matter will spontaneiously pop into existence out of nothing - a direct transformation of the vacuum energy into matter.
3) Combining 1) and 2), we could state that what we do see as trails is the direct effect of space compression by the ships engines, "creating" matter (in form of gas) out of vacuum energy.
The different colors are based on the created molecules, as different elements do interact differently with light - a fact used in all sorts of spectral analysis. (Okay, this is SF now and pure fantasy. But it fits, doen't it?)
I do not know though, if the matter creatred varies due to the ship's masses and are an inevitable physical consequence or if the engineers just went creative and thought, different colors migth be a fancy effect...
I hope, this does help!