1. Charles kills serveral people in 2028, including "some" of the X-Men. Not all of them are dead.
2. The Mutant-suppressing corn stops humans from producing offsprings with the X gene. No Mutant has been allegedly born for 25 years by 2029. However, we know that some have due to The New Mutants. The Essex Corp picks up mutants before they become known.
Honestly, Logan isn't that bad of a future, apart from the deaths of Logan and Charles. Less mutants mean less chance some crazy person could hypothetically be born with god-like powers and become a terrorist. Mutants aren't inherently bad people but every mutant is definitely a risk to both humans and other mutants, so controversially I kinda respect the corn thing because it doesn't actually hurt anyone. Unfortunately it appears that it was only done so that they could weaponize mutants themselves, typical Mr. Sinister behaviour.