I watched my $5.99 copy of the film last night, and I observed a few things which I think contributed to the film's failure.
The biggest problem is that the film is too dark. Like every movie these days, everything is dark. Whereas the original show was bright (even for B&W) and often took place in daylight. When the show changed to color, bright, primary colors were used which were eye-catching and interesting to look at (a staple of many 60s shows that were introducing color to audiences). The movie looks drab and too similar to every other movie of its era for it to stand out or be memorable. Same goes for all the computer screen imagery -- there were lots of glowing computer screens in dark rooms to give the movie that "techno" look. But it looks dated and strains for atmosphere, when the old show used clunky computers and big rooms for a futuristic look, which still looks more engaging that the glowing computer imagery and dark rooms of the movie.
(The latter day Star Trek projects are guilty of the same dark atmospheres. The original show and TNG were bright, optimistic shows that were visually interesting. Voyager and Enterprise were drab exercises in bleak surroundings where everything was in shadow.)
The much-discussed edits really ruin any chance the story had to be engaging. The way the film is cut, situations change abrasively and characters don't develop. Worst of all, you never get a sense you really know what is going on.
Lastly, much as I liked Fiennes and Thurman, they didn't have much chemistry, which is essential to this movie. Fiennes lacked Patrick Macnee's charm and his ability to always have a smile and a chuckle ready to diffuse a situation. Fiennes' character was sullen more often than not.
Overall, I'd say I enjoyed seeing it because I am a fan of the original show, and I can trace some of the elements in the movie to the show, but it doesn't have enough in common with the show for it to really be worthy of the name. As such, it is simply another Hollywood exercise in putting a famous brand-name on a product movie and hoping people will buy. Given the movie's dark tone and the show's bright optimism, I'm not surprised it failed.