Basically you have to decide what is most important to you. Do you want to have the widest range of content offerings(Roku), or the best compatibility between other Apple devices and software(Apple TV)?
The Roku box for example can play Hulu and Hulu Plus. The Hulu service is in very high demand and a very good content stream for the Roku. The Apple TV at this time will not play it out of the box, although it can be hacked to do so.
The biggest advantage that the Apple TV has is if you own or plan to use an iOS device in conjunction with it. For example, you can use AirPlay to stream music, photos, video, and apps to your Apple TV. This can be very handy in many situations. If you don't already have an iPhone, iPad, or the like - and don't plan on getting one anytime soon, then this shouldn't be a big draw.
The Apple TV also works flawlessly with iTunes. For example you can use iTunes Match then stream the audio to your Apple TV very easily. Roku can do some similar things with iTunes, but is does not have the same level of integration.
Overall, both devices have benefits and downsides, it just depends what you think your primary use will be and what hardware ecosystem you have. For more detailed information I would take a look at this review that compares the two.