Why is everyone so frightened of the Krogan?

As someone who never kills Wrex, always cures the genophage and always spares the queen, I still don't necessarily agree with everything you say.  For one, the very fact that Rachni who are separated from their queens will go insane and attack is reason enough to be distrustful.  Even if you believe the queen you might still think they're too easily weaponized.  Just thinking of the sheer volume of rachni in the Noveria facility is enough to give a person nightmares.

Second, Wrex and the Rachni Queen weren't exactly coming from the same place.  The queen couldn't have killed Shepard if she had wanted to regardless of Shepard's decision.  She probably understood that.  Hence, her only choice was to reason with Shepard and hope for the best.  Failing that, try to escape.  Wrex, on the other hand, is out, free and weaponized.  Had the Rachni Queen been similarly out and free she might have done the same thing.  From the in-game perspective, we just don't know.  What we do know is that Rachni threatened to destroy all beings in Council space.  Whether or not the krogan might have done the same, they didn't and proved incapable of doing so (since they failed).   Now, from playing ME3, I have learned that the Protheans were at fault for any kind of aggressive Rachni.  That doesn't necessarily help their case (because that means they're violent and aggressive) but does allow for a greater level of compassion.

Here's Wrex's viewpoint: he's watched the krogan continuously decline, watched all the in-fighting that has occurred as a result of hopeless krogan making terrible decisions, he's seen his own father turn on him...he attributes all of this behavior to the genophage.  As we learn in ME2 and ME3, Wrex knows what the krogan have been and believes they can be better.  That's why he gets so aggressive about it.  He'll also put his money where he mouth is in ME2 and ME3.  He takes over his clan, puts it in the forefront, and works hard to change krogan behavior.  With Eve in the mix in ME3, there's a bright future for the krogan.  Had Wrex really intended to shoot Shepard in ME1 he would simply have done it.  Instead, he reacted poorly but backed down if reasoned with because he understood that a cure in the hands of Saren would just lead to the enslavement and eventual death of the krogan.