I'm just pondering a situation recently where a sister and I were discussing the Shi'a practice of saying "Ya Ali madad" ("Oh Ali, help me"). (The topic of this post isn't on the Shi'a, btw, so don't focus on that. This can and does apply across the Muslim spectrum.)
Some folks accused us of being Salafis and pronouncing takfir on people (declaring who is and isn't Muslim) because we pointed out that Allah forbids calling upon other than Him in the very first chapter of Qur'an ("You (Allah) ALONE we turn to, You ALONE we seek for help"). They accused us of being intolerant. How, precisely, is it intolerant to remind people of one of the most basic teachings of Qur'an? Just because they don't like it doesn't make it any less the truth.
Is it okay to pronounce takfir on people? No. But recognizing it when their own words and behavior pronounce it on them? You're not judging them - they're announcing where they stand to you! There is a lot of stuff that Muslims "advise" each other on that is, frankly, stupid. A lot of things that are simply their own opinion of what is Islamic and what isn't, with no basis in Qur'an.
If you see a Muslim calling on other than Allah for help, then that's not pronouncing takfir. We are duty-bound to remind our brothers and sisters of Qur'an's teachings - especially when it relates to shirk, the most hated, most warned-against sin in the Qur'an! If they hate the reminder, there's nothing we can do about that.
As Muslims, if there is ANYTHING we should be paranoid about, it's shirk. The day we become lacksidaisical about shirk and excuse it among our Muslim brothers and sisters is the day we risk falling into it ourselves. Shirk is a very slippery slope.
I think that, sometimes, we can go to such lengths to give people the benefit of the doubt and not judge them, that we're actually risking being detrimental to our own selves, by surrounding ourselves with influences that can subtlely affect us (example here: Muslims who call on other than Allah for help). Does that make sense?
There has to be a happy medium - neither condemning everyone for "not thinking like me", but also not happily accepting it when our brothers and sisters say "La ilaha il Allah" and in the same breath seek aid with something/someone else.
I think that many people have reached a point where, in the name of tolerance, they're willing to ignore some serious issues and try to blow it off by calling it "a difference of opinion". We can have different interpretations of SO many things in Qur'an, and that's okay! Nothing wrong with difference of opinion, but there's a difference between that and attempting to change Islam.
There are some rules that are hard and fast. Not setting up partners with Allah is the bedrock of our faith - if we're willing to overlook it when our brothers and sisters are veering dangerously in the direction of shirk, if we're more afraid of hurting their feelings by reminding them of the Qur'an's teachings or them branding us as "intolerant" than we are of allowing them to go astray from tawhid, then we have a serious problem.
Sometimes Muslims think, by virtue of being Muslim, that they are impervious to shirk - that they could NEVER, no matter what they say or do, set up partners with Allah. We need to get over this erroneous notion, this arrogance that makes us think what others fall into isn't also a potential trap for us.
Being Quranist or Progressive doesn't mean we sit around the campfire singing Kumbaya, regardless of what our brothers and sisters in Islam are doing. There's difference of opinion and then there is clearly laid out Qur'anic "DO NOT DO THIS" criteria. People can turn away if they choose to do so, but why would any Muslim turn a blind eye to another Muslim doing something that falls within the realm of shirk? We love each other enough to nitpick over beards and hijabs and fingernails and socks, but not enough to remind one another of the Qur'an when we appear to have forgotten it? SubhanAllah....