This is a complex question, and the answer varies a lot over time and across the groups who might claim title to being 'atomic scientists.' I suspect you'll get a more detailed response from restricteddata soon, but here's a first-order summary:

On one hand, you had a sort of scientist elite who had been involved in the Manhattan Project, such as Oppenheimer, Teller, and others who got deeply involved in politics in the postwar period, trying to guide the government by taking on positions of authority in the Atomic Energy Commission, presidential advising committees, and so on. They eventually broke into factions along a number of issues, but very important among them whether or not to build a hydrogen bomb. To over-simplify, the anti-H-bomb crowd lost, and lost a lot of their influence in Washington, especially during the McCarthy era, while the pro-H-bomb crowd (notably, Edward Teller) took over the AEC and the massive funding authority that went with it. Teller was not the most level-headed guy, and for those who were increasingly upset over radioactive fallout and worried about nuclear war, he put a face to the archetype of the amoral scientist whose calculations could push us over the brink - similarly, Oppenheimer became a martyr for getting tossed from power for arguing for international control of atomic weapons.

Then there's a huge number of 'atomic scientists' who were less prominent in the Manhattan project, came after it had shut down, or were involved in other aspects of the science or engineering around the topic who also wanted political say, generally as part of the "scientists' movement" for international control of atomic weapons, or reduction in their numbers, or other 'pro-peace' / internationalist arguments. They founded a journal, the Bulletin of the Atomic Scientists, that was a fairly active voice of dissent throughout the Cold War buildups of atomic weapons.

There are a lot of other things going on here to track. The anti-nuclear movement really peaked late in the Cold War, but was around from pretty early on, and was a coalition of many scientists as well as grassroots activists who came at the issue from a lot of angles. Many of them deeply distrusted scientists, as you suggest. The issue of nuclear fallout and the start of 'environmentalism' made a big impact in things like the nuclear test ban treaty, so there people who would later be called environmental scientists were sometimes allied with the anti-nuclear crowd.

Some suggested readings:

-Anything by Hugh Gusterson

-Stuart Leslie, The Cold War and American Science

-Jessica Wang, American Science in an Age of Anxiety: Scientists, Anticommunism, and the Cold War

-Wellock, Critical Masses

I would periodize it roughly like this, using very crude categories like "liberal/conservative" and "hawkish/dovish" to reflect both the roughness of this characterization and the kinds of categories that these nuances were boiled down to at the time:

• In the 1940s, the "atomic scientists" were mostly glorified and held up as people who needed to be listened to and respected. Generally speaking the reaction was pretty positive no matter what one's politics were.

• In the 1950s, the situation gets more polarized. You get a split between the hawkish scientists like Teller, and the more dovish scientists of the Oppenheimer stripe. For Cold War liberals, the dovish ones are seen as the ones to listen to and the hawkish ones are seen as maniacs. For Cold War conservatives, the dovish ones are seen as potential spies, the hawkish ones are the ones to listen to.

• In the early to mid 1960s, the tensions cool a bit but are still more or less present.

• By the late 1960s and early 1970s, you get a strong rejection from the New Left and by youth in general of all of the atomic scientists. They're all warmongers, weapons makers, etc. in this view. This approach makes no distinction between the hawkish and the dovish ones of the earlier period (much to the confusion and anger of the dovish scientists like I.I. Rabi who get lumped in with people like Teller).

• By the 1980s you get further polarization again, with the dovish, non-governmental scientists criticizing those who worked in the weapons laboratories and promoted controversial things like the Strategic Defense Initiative.

• By the 1990s, most of this cools down considerably with the end of the Cold War.