There is no evidence that Franklin ever said that beer is proof that God loves us and wants us to be happy. Even though that quote is attributed to him on tee-shirts hanging in the gift shops of 90% of breweries, there's no source attributing it to him. There are so many sources that use this quote that it is easy to understand when someone believes it to be true. While the founding father was quite prolific, his writings do include a quote that is similar to the one related to beer. In a 1779 letter to his friend Andre Morellet (translated from the French), Franklin did write:
"Behold the rain which descends from heaven upon our vineyards, and which incorporates itself with the grapes to be changed into wine; a constant proof that God loves us, and loves to see us happy."
It is sort of the same sentiment and it is understandable that someone, some time back, was trying to remember that thing Franklin said about some alcoholic drink and, without double-checking the source, came up with a misquote about beer.
So, it seems quite likely that a few understandable mistakes led to many people deciding to misquote Franklin. This little mistake is not likely to profoundly affect the course of human history or anything so drastic but, still, it's best to use factual information, especially when there is written proof of what he actually said.
Ben Franklin and Beer
It would be foolish to merely speculate about Mr. Franklin's personal feelings or culinary opinions about beer because there is very little supporting evidence. Anyone who has read the Autobiography of Benjamin Franklin might recall the author's strong objection to his coworkers' habitual intake of "strong" beer.
When he was working in a London printing house as a young man, Franklin observed that all the men working around him were "great guzzlers of beer." Franklin himself drank only water (during the workday, at least). He also noted their surprise that, despite their daily regimen of strong beer, they weren't actually as physically strong as Franklin: he could carry two heavy forms of type up and down the stairs; the others carried just one.
Franklin tried to disabuse some of his coworkers of their belief that beer made them strong. Some took his advice, but most did not. His reasoning was simple: beer muddles your thinking, provides little nutrition, and slows you down. It also costs money, which the printers were reminded of each week when they saw their wages docked for beer expenses.
Needless to say, Benjamin Franklin was successful in his job at the London printing house, as he was with pretty much everything else in his life. So if you want to take away a little beer wisdom from the great man, don't drink beer at work; drink water instead.