Governments are using cost-benefit analyses all the time to decide whether they should invest tax-payer money in this and that project. Private individuals are never making any decision at that level. I agree that this money could have been spent otherwise, but this holds for any single project funded by a government, doesn't it?
Coming back to the LHC money, it consists at the end only of a small fraction of the money of a state. I recall that this number is integrated over more than 30 years. Fundamental science experiments are hence cheap (compared to a state budget) and could bring a lot in decades. And even if they are not bringing anything, some benefits (even if they are small) are there. This is the point I wanted to show.

Concerning the second point of your post, I am not sure to follow.
Which loss of freedom? This I do not understand at all.
Then, knowledge is not centralized: all CERN's results are publicly available and data is stored world-wide and will be made publicly available in the future (some pieces of data is already there on the web). IMO, this is not really what one could call a centralized knowledge.
Finally, to comment on the third point, at the political level, they are many discussions within the community about experiments that should be run, in particular from the scientific standpoint (we are now discussing the next generation of collider experiments). At the end, the community will decide what is good for it (and this does not mean one single experiment).