In general code names were randomly selected from an Inter-Services Code-Word Index, a list originally taken from a dictionary, sometimes with intervention such as Churchill personally selecting "Overlord" ([The Art of Naming Operations] (http://strategicstudiesinstitute.army.mil/pubs/parameters/Articles/1995/sieminsk.htm), Gregory C. Sieminski). There's a section in Monty and Rommel: Parallel Lives by Peter Caddick-Adams on the Normandy beach code names:

The British beach names, Gold, Jelly and Sword - all types of fish - were the original choices, but Churchill disapproved of the word Jelly for a beach on which many men might die, so he had the word changed to Juno.

Unfortunately he doesn't give a source; it's plausible, in keeping with a 1943 memo from Churchill in which he said code names ought not to be "... of a frivolous character, such as "Bunnyhug," "Billingsgate," "Aperitif," and "Ballyhoo."" (Churchill By Himself), but I haven't seen anything else to corroborate "Jelly" being an original selection.

Caddick-Adams continues:

Omaha and later Utah were named after the birthplaces of the US V and VII Corps commanders 'Gee' Gerow and 'Lightning Joe' Collins.

This is less likely, as Gerow and Collins were from Virginia and Louisiana respectively. An [article in the Omaha World-Herald from 2008] (http://www.omaha.com/news/military/d-day-was-omaha-beach-named-in-honor-of-local/article_5b631178-e2cc-11e3-a695-0017a43b2370.html) offers the possibility that it may have been the home states of two carpenters building Omar Bradley's headquarters that resulted in the names, or the beaches being named after naval units assigned to the areas; there doesn't seem to be a definitive account of the selection of the names.