The space truckers in Alien were smarter than all of the characters in the prequels.
The USCM squad were smarter than all the characters in the prequels, albeit far more arrogant and ill prepared.
The space truckers tried to take all the right precautions, Ash just (purposefully) mucked everything up.
The reason the marines are ill prepared in the movie seems pretty obvious to me. No one believes Ripley's account of what happened and they've also probably never encountered anything like the Alien before. That coupled with the fact the colony hadn't found anything like what she described (Prior to Burkes message) makes the scenario believable to me.
Even if they did believe here I don't think they'd have anything to properly combat/prevent what she described, but if we follow the EU (specifically Berserker) we know that they did develop weapons and equipment (Teape's deploy-able mask, the actual Berserker unit) as an answer to the Alien.
Certain character choices in Prometheus are pretty stupid after you watch it more than once. Scientists choosing to take off their helmets and breathe alien air is one of the most glaring to me. It would have been just as easy for them to write that someones helmet cracked, or they were running low on oxygen and a crew member chose to take the risk rather than die (ala Red Planet).
I give the biologist a little bit of a pass for getting close to the hammerpede, but only because he seemed to let his excitement get the better of him. Still a stupid choice though.
The same argument can easily be made for the first half of Covenant. Colonists or not, they really should have treated the situation with more caution. Admittedly I don't remember what scans they did, but do we know if the scans also accounted for something microbial/viral? Or if it also picked up wild life?
I mean I wouldn't want to go down to the surface of a planet without for sure knowing something in the water/air wont kill me, or without knowing that there's something down there like an alien brown recluse whose bite wont melt half my flesh off.