Regarding the indiscriminate feature of a drone strike: We are all well are aren't we that the bad guys we target in Afghanistan, Pakistan and Yemen intentionally mingle themselves in with innocents with the understanding they too will be killed and the subsequent negative press and perceptions follow. They (terrorists) have few ways to counter drone attacks, and so the only means they have is to make it as costly for us execute.
As far as what's taken for "bad," this is a sort of chicken and egg discussion. If the US had a deeper history and more support in Pakistan (toss in a smidge of Afghanistan support/Pashtun tribes as the three are not entirely separate groups), and if the US was willing to risk more boots on the ground, then it wouldn't need to rely so heavily on drones to begin with.
However the US doesn't have those things. It isn't fixing those things very well. It has a messy diplomatic status in the region. The drone campaign isn't improving locals' views of the US, and again: We're not putting people on the line (either in rural Pakistan, or on the cosmopolitan international news/policy circuit) to fix that.
Despite the fact that the CIA may be waging the most precise “bombing” campaign in history, it is nonetheless alienating millions of average Pakistanis. Pakistanis are prone to conspiracy theories and there is little chance that U.S.-based researchers can shift the paradigm in this country that drones almost exclusively kill innocent Pakistani civilians.
Moreover, as long as the U.S. government continues to conduct the campaign in secret, refusing to divulge any information on it or even acknowledge that it carries out these strikes at all, its officials cannot even enter the conversation. Unfortunately, as Christine Fair has observed, this leaves the field free for the very groups who are being targeted to report the impacts on the ground and to frame the strikes for the Pakistani public.  In-so-far as the American objective is to isolate and degrade Al-Qaeda, the Taliban and their affiliates, this represents a serious problem.  To the degree the target groups are able to disseminate a common sense of victimhood to the Pakistani public, it is America rather than its enemies which is likely to be increasingly isolated in the Pakistani political conversation. Thus, for all the best intentions, the unprecedentedly accurate covert CIA drone strikes may lead to a strategic setback even as they gain a tactical success by surgically killing hundreds of FATA-based Taliban and Al-Qaeda extremists every year.
Sounds like the sort of game we played and lost with Ho Chi Minh: There's no question the US can keep on bombing, provided there are bases and Pakistani military doesn't intervene (unless someone cut the funding, or domestic opinion gets fed up). All that remains to be seen, is just how much support Al Qaeda/Taliban etc. can draw regardless -- or partly even because
of the same bombing -- and for how long.
In short, the US isn't especially willing to take risks with personnel when there's a distanced technical solution. It isn't willing to come down off the high horse, release more data on sensitive technology, and discuss or "negotiate" how people in other circumstances -- whether civilian or militant -- actually experience and perceive remote bombings. So naturally, the guerrillas do what they can in response. American coldness and "body count" cost-benefit analysis on the issue comes off in Pakistan as aloofness and exceptionalism.
I'm also not clear that the guerrillas really have options other than to shelter with civilians and/or sympathetic locals. The area is highly rugged terrain. The US drones are going to come down hard on any suspected target camp they find, assuming they aren't saving too many people for negotiation or bribery potential. What else are people scurrying around in the mountains for weeks going to do, if they don't take shelter in populated areas? If the area resembles other steep parts of Pakistan that I've seen, there are really not that many choices of where to stay -- at least in the more rural parts. I suppose they could disperse more and live off the land for a time, but it could be difficult to supply and coordinate operations that way. But once you have a guerrilla operation where you have to stay even partially dispersed and you're technically outgunned, I think none of this is really surprising.
So as to who's the "bad guy" since it seems you must have just one... The US can operate with relative impunity in sending bombs after its opponents... They tend to regard that as "bad" too, I think. Is it good and "moral" to expect them to capitulate on all their goals because they can't survive and fight without involving a local population? Even while the US can't bomb without at least sometimes striking the same population? I think that question is more about what you see as worth fighting for -- and less about how the fighting is done.