This problem will not be solved by debating over the minutiae of whether "calling someone a kafir makes someone a kafir, so Sunnis are a kafir." Of course, you can discuss it, and it could be good to discuss it historically and religiously.

However, it is an excuse being put forward for a viewpoint, and if this excuse is disproved, another one will be presented.

The problem here is mindset, in particular,
(a) lack of understanding of the Prophetic message and how the Prophet (S) reached out to all people rather than excluding people to form an elite group,

(b) arrogance and egotism - thinking that one is part of the small, elite, saved group while everyone else is wrong floats one's ego, and is one of the subtler traps of Shaytan, 

(c) a misunderstanding of the nature of Allah. Allah, as the creator of the universe, including the human being, is not so petty to kick people out of the ummah because of a handful of historical errors.

Sometimes also (d) some individiuals are benefitting from these ideologies, such as if they get followers or fans from spreading them and appealing to people's sense of clannishness.

To be fair there may also be (e) backlash against the Sunnis who call Shiis kafir and use that as an excuse for violence.

Surely we can understand that just as it is wrong for Sunnis to declare Shiis kafir, it is wrong to declare Sunnis kafir. We should treat others as we would like to be treated.

So basically these are the things that really need to addressed. A person who has humility before Allah and is not using their religious identity to bolster their own nafs or ego will not take it upon themself to decree masses of sincere people as kaafir.

Sometimes this takes time, such as years, and it won't happen in one or two sessions.