The real problem is, when all you (think you) see every day are "baddies", it's too easy to forget that the vast, vast majority of the world are not "baddies", and that what might, possibly, in the right light be suspicious behaviour for a "baddy" isn't even slightly suspicious most of the time. From there flows a slightly paranoid mindset of "we must stop ALL the evil in the world at any cost".
This is compounded by the fact that they appear to have rather less accountability than the typical civil servant. Some elements (but by no means all) do like it that way and actively campaign to limit any increase in oversight because (as they see it) "making our job harder makes the world less safe".
You often see the same thing in law enforcement and it's very hard to protect against that culture over the long term. We don't have enough people in politics or government who are willing to say "this will make your job harder but it's not worth doing unless you do it ethically".
Good.
GCHQ are not there to protect the interestes of British citizens, they are there to enforce the status quo of the ruling class and engage in economic espionage.
So many of there operations are counter to democratic principles, I'd prefer them underfunded and ineffective than funded and potent.