"Iran having a nuclear weapons program is a bad thing.

Iran NOT having a nuclear weapons program is a bad thing.

I guess I must be kind of slow. I don't get it."

We had reason to suspect that Iran had a nuclear weapons program. US intelligences now appears to believes that Iran had a nuclear weapons program, but it was suspended in 2003.
If the nuclear weapon program was indeed suspended [entirely] then that is good news. It was still bad news that Iran had a nuclear weapon program.
I think we can easily forgive, that Iran starting a nuclear weapon program considering all that going on in that region and if we can get enough verification that indeed Iran has stopped it's nuclear weapon program [having a nuclear weapon program violates the agreement that allows other countries, such Russia and China, to help Iran in a peaceful use of nuclear energy] then that would be even better news.

Along with verification I would imagine that one of our focuses, should be make ensure that nuclear safety is a high priority in Iran [as well as in India and Pakistan].