I'm not "OK" with what happened to Padilla, but the contention was that the executive branch "has been given the power" to indefinitely detain U.S. citizens, and that assertion is false.

Read the history of the Padilla case: http://www.nyclu.org/case/padilla-v-bushhamdi-v-rumsfeld-cha....

See also: http://www.cato.org/publications/commentary/what-supreme-cou....

There was a legal wrangling over the scope of the President's detention powers, and Padilla's appeal to the Supreme Court was rendered moot by the government deciding to charge him. No U.S. citizen has been indefinitely detained since.