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The guy was an illegal immigrant who did not know English and ignored repeated commands to stop running, drop his heavy knapsack, and raise his hands.

If you are going to live in a country it is your responsibility to know the language and comply with that country's officials' instructions, it is not the job of the police to intuit that you are a "good" criminal (illegal immigrant) instead of a "bad" criminal (terrorist).

"In his first public comments on the incident, Mr Livock said that while the tube, which he had boarded at Clapham North, was waiting at Stockwell station, he heard shouts from outside of something like "he's here". Seconds later, a man entered the carriage and pointed a gun at Mr de Menezes, he said.
Asked by Nicholas Hilliard QC, counsel to the inquest, "Did you hear him saying anything to Mr de Menezes?" Mr Livock said: "Absolutely not."
Mr Livock earlier said that at first he had thought that the group of plain-clothes officers, who were wielding guns when they ran on to the Tube at Stockwell, might be "a group of lads who were just having a laugh".
He said that he and his girlfriend, Rachel Wilson, who was with him, only realised something more serious was taking place when Mr de Menezes was shot dead at point blank range. "One of my initial thoughts was it was all a game and they were a group of lads who were just having a laugh - a very bad taste laugh but just having a game on the Tube, because they were just dressed in jeans and t-shirts but with firearms," Mr Livock said.
Mr Hilliard asked: "Had you heard anything said about police?"
Mr Livock replied: "No, certainly not. And I remember that specifically because one of the conversations that Rachel and I had afterwards was that we had no idea whether these were police, whether they were terrorists, whether they were somebody else. We just had no idea."

The Telegraph 2008