Why do the aliens see things as green or red?

The logic is simple. The color of the objects change according to whether it is harmful or not to the aliens or the aliens want to attack it or not. Now we have to think deeper in this.

The color is "Green" when the object is not harmful in its true sense, meaning if the object is a human being, he should not think evil. We see Hopper had an evil plan to attack the alien in another way. The alien might have perceived it. So he maintained red-alert for him.
In case of the cannons, if the direction of them is towards the alien ship, it was shown as "danger" meaning it might fire upon them. The machinegun was never seen by alien ship (I think because the boat was too small to be seen), until it started firing upon the ship. Then they looked at it and it was seen as "red" (as it was firing). In case of pillars, like I said, the alines saw "red", if the object seen is meant to be attacked on. The pillars were meant to be attacked, so it was seen "red".

To question your query to why they did not attack the earth, I would rather say the plan "That they were going to need another planet" was just a mere guessing by Harper. It is not confirmed in the movie. So it might not be true. And that whatever they attacked on earth might be just a precaution, so that the human do not try to attack them.