In Act 3, Scene 1 of Julius Caesar why did Popilius say, 'I wish your enterprise today will thrive'? What do these words mean?

The effect of Popilius' words is to add further to the dramatic tension leading up to the assassination. Popilius means exactly what he says. He knows that Cassius and a number of other conspirators are going to try to kill Julius Caesar and he is wishing him good luck. Why would Popilius want to wish Cassius good luck or to say anything at all? Popilius is playing it safe. He wants to be recognized as a supporter of the conspirators because he assumes there will be a lot of "collateral" bloodshed after the event, and he doesn't want to be one of the people he expects to be eliminated as a sympathizer of Caesar. On the other hand, if the enterprise doesn't "thrive," then Popilius would prefer not to be known as one of its supporters. That is why he only speaks in guarded terms to one person, to Cassius. But he obviously knows a lot, including the fact that Cassius is the instigator of the assassination plot.

Cassius has been recruiting people to take part in assassinating Caesar since before the play even began. It was inevitable that word should get around that there was such a conspiracy brewing and that Cassius was behind it. Some of the people Cassius approached who declined to get involved would still know about it and might very well mention it to others. So there could be a number of people in the crowd who expect an assassination attempt to occur, but Popilius is smart enough to work both sides of the street, so to speak. He is looking ahead. He wants to be on the side of whoever ends up holding the power in Rome. Right after Popilius talks to Cassius and alarms him, Brutus observes:

Cassius, be constant.
Popilius Lena speaks not of our purposes;
For, look, he smiles, and Caesar doth not change.

So Popilius goes to Cassius to hint broadly that he is a sympathizer, and then he goes directly to Julius Caesar, probably to assure him of his good will and to say that he hopes Caesar's "enterprise will thrive," i.e., he hopes Caesar will be crowned king that morning. 

It is probably worth noting that when Antony, Octavius, and Lepidus have seized power and are choosing the men they will exterminate because of their sympathies with the assassins, the name of Popilius Lena does not come up. He may have been able to save himself by his foresight.