You probably also remember how the war ended ten years later, when the Trojans received a huge wooden horse and brought it into the city. But the horse was hollow, filled with Greek soldiers, who waited until dark to sneak out, kill the Trojan guards, and open the city gates. The war ended quickly after that: the Greeks massacred the Trojans, burned Troy, and divided the spoils.
So why would a condom manufacturer risk comparison of its product to something that looks appealing but is going to burst with harmful agents who will sneak past your defenses and plunder your resources once you invite it inside? Isn't that the opposite of what a condom is supposed to do?
Apparently it's not always a bad thing when your brand name is associated with something that has negative connotations. In Jonathan Swift's novel Gulliver's Travels (1726), a 'yahoo' is a filthy, savage humanoid. Today, the word 'yahoo' means a crude, brutish or obscenely coarse person or an expression of excitement. It's also the name of a multinational internet corporation. Having a negative connotation can make a name more memorable, help it stand out among competitors, or suggest a reputation for being edgy.
So maybe 'Trojan' isn't such a bad name for a condom brand after all. And any additional association with the words 'huge', 'wood', or 'horse' probably doesn't hurt.