It looks like that at the time, the decision whether to fly over the area or not was a judgment call. In hindsight some companies got it terribly wrong. From Wikipedia:

Some airlines had avoided eastern Ukrainian airspace prior to the MH17 shootdown, while many others, including 62 operators from 32 countries, had continued to fly routes over the region.

Your statement "I mean dudes setting up antiaircraft weapons in random fields ..." gives somewhat incorrect impression.

What is known is that a Buk 9M38 surface to air missile system belonging to the 53rd Anti-Aircraft Missile Brigade was deployed by pro Russian separatists in the Torez area.