According to Superman: The High-Flying History of America's Most Enduring Hero the man of steel got too close to secrets about the development of the United States nuclear weapons. At the time the public was fascinated with all things atomic, radium infused water, radioactive chemistry sets, etc.

Cyclotrons have a few uses, but in this case the concern was probably over possibly causing closer scrutiny of how they could be used to separate isotopes of Uranium for enrichment, which the US was doing on an industrial scale at Y-12.

E.O. Lawrence E.O. Lawrence (of LLNL fame) standing over part of a Cyclotron.

Excerpt courtesy of Google: