If you "rolled over" the money within 60 days of receiving it, then you can indicate in the 1099-R interview that you rolled it over to a qualifying IRA. This will remove the tax and the penalty.
After you enter the 1099-R (please enter all fields as they are shown on the 1099-R), continue the interview. You will come to a screen entitled "What Did You Do With The Money From [the name of the place on your 1099-R]". On this screen, check that "I moved the money to another retirement account".
Then indicate whether you rolled over some or all of the money.
