Cryptic has poster a response to the Skill Point Cap Issue in the official forums:

Star Trek Online Forums - View Single Post - People are going to qut if you limit skill points...SP People look inside.

Hey gang,

I know quite a few of you are upset over this, so let me try and explain this change to you.

We have plans to release more content in the future, and at some point we'd like to raise the skill point cap, in the same way other titles have raised their level cap. The skill point cap is in place to ensure that we can not only add more content later on, but also to make sure that we can balance that content to provide you with a suitable challenge. With a skill point cap in place, we know what you're capable of, and we can balance the challenges in new content to provide you a suitable challenge. With no skill point cap, you'll not only be able to max out every skill in the game, but eventually, when we release new content, it will become trivial to you immediately. When we raise the level cap, you’d be max level right away. In the end, not having a skill point cap hurts the game, and consequently the amount of fun you guys can have.

Star Trek Online is also unique in that your Captain isn’t the end of your avatar. You’ve got Bridge Officers to tinker with, who gain skills on their own. You’ve also got a great number of ships available to you, and all sorts of weapons, consoles and devices to discover and utilize. So even though we made the decision to cap your Captain’s skill gain, it doesn’t mean there’s not more to achieve in the Star Trek Online universe at max level. In fact, we’ve got all sorts of stuff planned, from raid-style Episodes to more Fleet Actions to more Star Clusters. We’ll be talking more about what’s coming post-launch soon.

So yes, much like other MMOs, there is a cap as to how far you can advance your character at launch. Much like other titles, there are also other incentives to keep players invested in the game once they reach that cap. Endgame content is going to have some pretty cool rewards that players will need in order to actually "max out" their characters, everything from more Kits for your captain, to new equipment for your ship, and there's also some really cool powerful Bridge Officers to find out there as well.