Cartoon shows featuring a main character and his dumb bosom buddy have been around since Crusader Rabbit in the 1950s. People love to spoil it by making something more out of their tight relationship than was intended by the animators. Were Rocky & Bullwinkle gay? Fred & Barney? Okay, maybe Ren & Stimpy were more than chums, but that show was really off-the-wall anyway.
I don't believe that Spongebob & Patrick are lovers; they're occasionally too girlie sometimes, but I think that's supposed to be funny, not suggestive.