This is not a question with only one answer as a few things were going on at that time.
1. The British press sometimes behave in nasty ways sometimes and
are inclined to build people up then try and then kick them down again so the adverse publicity (true or invented) could have had some influence on the voting.
2. Diversity were very very good, let's not take anything away
from them. They had an excellent coreographer plus a couple of
very cute young kids (always good for votes).
3. A lot of people here do not like excessive hype and there were quite a lot of people thinking she would walk it so perhaps they
thought "why bother to vote as she will win anyway". I tried to vote but after about 10 tries I couldn't get through so gave up (was I the only one?).
I think that bearing in mind the mental state Susan was in, comming second may have been the best outcome for her (not so much pressure to cope with). She was definitely the best singer by miles and there is no way that a group of dancers would ever get a recording contract so she still has an excellent chance to have her dream come true and seeing clips of her on the BGT tour, she seems to be enjoying every moment of it thank goodness.
Links:
[1] http://www.susanboylefanclub.com/node/1106
[2] http://www.susanboylefanclub.com/node/1098