Dominic West won the award for best Actor for his portrayal of Fred West, a serial killer in Britain. Whilst I haven't seen the show myself I can surmise what were the contributing factors here.

Ben portrayed a character that had many interpretations to look back on as well as the original canon to serve as a reference point for building this character into what we saw on TV.
Dominic on the other hand portrayed an infamous real person who really had not been portrayed to this point on film. He would have relied on the script & his own research of news archives etc to build a character.
One of the hardest roles an actor plays is that of a real life character, dead or alive. The story itself was a heart wrenching, emotional one still fresh in many peoples' minds.

The Baftas are not voted on by the public, but by an independent jury so popularity holds no say in who wins at all.

I doubt Ben will be too worried about it, many brilliant actors from the past have been beaten for awards. One of my favourites, Meryl Streep had 20 years and many brilliant performances between her Oscars.