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In The Matrix, we can see that it is possible to make simulated worlds or rooms in which the characters can train their minds. We also learn that these worlds/rooms, as well as the Matrix, are not real. If these worlds are not real, it is possible to bend them as we see fit. It means that we can avoid having injuries.

It is possible to get hurt if we believe in the rules and do not attempt to break them, but why isn't Neo and his team breaking the rules when he fights against the Agents?

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There really is no great answer to that question. Mostly so there would actually be peril. But if I had to give a real answer I would refer you to a certain quote from Morpheus:

(Dojo)
Morpheus: ... What you must learn is that these rules are no different that the rules of a computer system. Some of them can be bent. Others can be broken. Understand? ...

The Matrix transcript

I would assume that injury falls under the bent category, they probably bend the rules of pain/death as Neo takes hits that would definitely end a fight if not kill you.

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    Stamina would be an example of a rule that can be bent. "You think that's air you're breathing now?" - Morpheus
    – Robotnik
    Dec 30, 2012 at 13:26
  • In the 'jumping' scene they rewrite that world so that people aren't killed by falling - but Neo isn't aware of that until he hits the ground so there's a contradiction there
    – user8416
    Jan 2, 2013 at 12:04
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This was never concretely explained in any of the canon media I know of, but I do have a theory.

Morpheus explains the following two things about the Matrix:

  • The Matrix is built on rules, but some rules can be bent or broken.
  • The mind makes any injuries that occur in the Matrix also occur in reality, because the mind is inseparable from the body.

As such, I think part of the reason for him being unable to break the rules around being injured is that the rules around injury cannot be fully broken. Note that they are bent on occasion, like when he stops a sword with his hand and only suffers a minor cut, during the fight with the Merovingian's goons. Furthermore, I would suspect that the true creator of the core rules around injury and death is the mind, not the Matrix, which would explain why Neo was incapable of completely breaking them.

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  • Actually, at the end of Revolutions, when Neo fights Smith, he simply refuses to die and thus stays alive. He breaks the rules increasingly well throughout the films and finally is completely free of them --- all of them.
    – bitmask
    Dec 30, 2012 at 17:27
  • I'm not sure anything in that scene counts for the rest of the movie, though, since the Matrix has become so corrupted by Smith's duplication. On top of that, the machines are using his body as a conduit to defeat Smith, so he would (assumedly) have increased real-world resistance to injury.
    – Polynomial
    Dec 30, 2012 at 17:41
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Because your mind makes it real:

"If real is what you can feel, smell, taste and see, then 'real' is simply electrical signals interpreted by your brain" Morpheus

Of course if you set your mind free you should be able to break those rules, just like Neo did.

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The last Matrix movie clearly shows the zion/matrix reality is indeed a simulation inside a simulation and one plausible explication to "Why is it possible to get hurt in the Matrix?" is that it's a bug.

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    plausible ?.. if you put an answer dont put plausible things cause this should be a comment
    – Rocket
    Jan 28, 2015 at 3:00

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