A writer always wants to put himself or herself into a story; writing is, after all, an expression of oneself. One's fantasies, demons, dreams, or opinions. Sometimes, that means a story will reflect your emotional or moral reaction to the real world around you, whether intentionally or not.
Sometimes, allegorical representations of current events and people in fiction is blatantly obvious to the reader. Take Lewis Carroll's "Alice in Wonderland" for example. Though now a classic in childhood fantasy adventure, its original allegorical meaning lost to time, Carroll's contemporary audience had no trouble seeing through his allegorical references and all-too-obvious symbolism. That didn't make his work any less enjoyable, though.We all know the challenge of allegory: not to sound preachy or self-righteous. Above all, not to sacrifice literary quality or entertainment value for the sake of getting your point across. The best allegory is the kind that slips under the reader's defenses, delivering a message without letting the reader know it. Until its too late for the reader to shut it out. That's the game between writer and reader.
Sometimes, if a story is exceptionally good, a reader might even forgive the most blatantly obvious political or social metaphor. Everyone knew exactly what the writers had in mind when the classic "Star Trek" episode "Let That Be Your Last Battlefield" aired about a year after the Watts riots. Two men, one a policeman, the other a radical, who despised each other with a flaming passion, simply because their half-white, half-black skin coloring was reversed. A stark and obvious symbolic representation of the absurdity of racism. It worked because it was so obvious, and so direct, building through passionate hatred and all-too-familiar scenes to its inevitable and tragic end. Sometimes honesty can work more effectively than cleverness in reaching an audience.
The most important thing, I believe is to be honest with yourself. If you've got something inside you that's screaming to get out, then let it out, no matter what. Then, find a way to tame the beast so it can reach an audience. I've approached issues that I felt strongly about through fiction. Sometimes an editor will reject such a story, saying it "drowns in the politics." And, others will accept it, focusing on the texture of the story itself. As with anything else, it pretty much depends on what the reader wants to see.
Odds are you're not going to convert anybody to your way of thinking. But, if you can effectively convey your opinion ... more importantly, your passion about an issue... and keep the reader entertained at the same time, even if he disagrees with you, then you've beat the challenge.