Why do we prefer visually aligned objects? We all know visual alignment is one of the foundations of design. Everything must be aligned with everything else.
We also know that when things are aligned it is easier to process information.
My question is why?

Nothing in nature is "aligned". What's the anthropological/biology reason why humans prefer aligned information?
One of the main reasons related to the 'Gestalt principles' 


Law of Proximity Objects near each other tend to be grouped together.
Law of Similarity Similar items tend to be grouped together.
Law of Closure Objects grouped together are seen as a whole.
Law of Continuity Lines are seen as following the smoothest path.
Law of Common Region Items in similar areas tend to be grouped
together.
Law of Connectedness Items that are connected are seen as groups.


This is a nice summary from the article referenced below:


  Coupling emotional and behavioral triggers in some form of cognitive grouping — whether by proximity, similarity or something else — strengthens the motivation to act on the behavioral cue.


I'd add to this: We feel more comfortable when perceiving something expected. When something breaks this (such as misalignment), it causes stress because there is a gap between our expectations (as the principles outline) and our experience. 

References


http://www.webdesignerdepot.com/2011/08/strengthening-behavioral-cues-in-ux-web-design-with-gestalt-principles/
http://graphicdesign.spokanefalls.edu/tutorials/process/gestaltprinciples/gestaltprinc.htm