For a Traveller game, you've got a lot of options about just what sort of game you're going to run. While many of the canonical adventures set the PCs as more-or-less loyal Imperial citizens (with commensurate opposition), there are any number of other ways to play it, and then the "bad guys" fall naturally into place, defined as "those who oppose your goals". Your differences with them may be largely philosophical, in which case, violence is likely to only be a last resort; it may also happen that your PCs will be diametrically opposed to the beliefs and actions of their antagonists, with no possible compromise or reconciliation... in which case, violence is likely to erupt.
As the GM, you need to define where you want this game to go. If you want gritty, bloody action, where betrayal is commonplace and nobody survives unscathed... you can play it that way. If you want to play something more like "Wuthering Heights" meets "The Amazing Race", you can play it that way, too. Think about what your players will enjoy, too, as there's nothing quite so disheartening as putting hours and hours of labor into an intricate plot, just to have your players say, "Ahhh, forget it, let's go start a bar fight and then get laid".
If your players are up for a "scrappy merchants barely getting by" sort of game, there isn't a lot of room for high-level politics, or fourteen different kinds of aliens. For a game like this, their opposition will be whoever is getting in the way of them making the money they need in order to survive, and that could be rival merchants, pirates, greedy officials, corrupt politicians, or even a large corporation intent on solidifying its control over the area. The location and time frame you choose to set your game in will also affect things; if you're on the Solomani Rim, you're likely to only see a mention of the Fifth Frontier War in the back pages of the news, and it certainly won't have anything to do with your existence. However, if your ship is based on Jewell, with your friends, family, and established contacts there, then you certainly WILL care about the progress and the aftermath of the Frontier Wars.
If you're going to run a "get lots of stuff, and if you ever see the same NPC twice, you know the GM is setting you up for a kill; always outrun word of your coming and your past atrocities" type of game, then have fun, and pick an opponent that will at least provide an interesting challenge.
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