I think most of the hatred is more hatred directed to Senator Jar Jar and originates from when he was found during the battle of Naboo by Jedi Master Qui-Gon Jin. Jar Jar is considered by many to be annoying and since Jar Jar is the most well known gungan in galactic history, most consider all gungans to be similar. The hatred of gungans is further solidified by anti-imperalists because Jar Jar was the main supporter of granting Chancellor Palpatine supreme power leading to the fall of the Republic and the founding of the Empire.