The Flash [Season 1] Why does everyone act like their own timeline is being reset in the season

[gameofarrowvers]

In the season 1 finale, Stein and Cisco basically confirm that they are living in alternate reality (Cisco says "so what you're saying is that we're living in a parallel universe?") So if Barry had saved his mother after travelling to the past via the wormhole, he would've created a new timeline where Nora lived, and upon returning via the wormhole, he would be back in STAR Labs, in the same timeline where Nora was killed by RF. What I don't understand is why everyone was acting like if Nora was saved then that would result in their OWN timeline being altered, as opposed to creating an alternate one, for example Iris says to Barry "I hope whatever life you get, it's enough for you" and Caitlin and Ronnie get married (assuming since they thought they'd never get the chance if the timeline was changed.) Cisco made it clear that they'd create an alternate timeline, so either Cisco's comment is a plot hole and there's just one timeline and not alternate ones, of everyone is just really dumb?
When Eobard travels to 2000 to kill young Barry, the timeline he travels to ends up being the one where Nora is killed, so by the same logic, the timeline Barry travels to would be the one where Nora is saved, rather than the timeline he came from before travelling through the wormhole, so why does everyone think their timeline is being changed!?

 

[Headliner]

Wells/Thawne said that time is very sensitivitie. If one event is changed, it can have severe consequences on many other time related things. Personally, I think Thawne was setting Barry up. Thawne's plan may have for Barry to save his mom which messes up the timeline and Barry never comes the Flash.