Yes, Earth and the rest of the solar system is protected, at least from cosmic rays by the solar wind (and the magnetic field it contains) of our Sun.

Essentially, the solar wind acts as a sort of bubble-shaped shield that deflects some of these high-energy particles. The solar wind also affects other extra-solar objects, though not necessarily enough to protect Earth from them. For instance, solar wind causes the ion tail of a comet , ablates bodies that lack protective magnetic fields, and can even produce water in space dust when the H+ ions bond with OH- groups in the minerals. There is also the radiation pressure from the charged particles. This is quite weak, but may be sufficient to push some very small particles out of the solar system, and also pushes the dust tail of a comet so that it points not quite directly away from the sun.

Solar magnetic storms are what create solar flares. Solar flares are very low-density plasma, which means that they wouldn't do much slamming into the Earth's atmosphere to living things on the surface. Over time, however, they could conceivably strip the atmosphere off if they weren't robbed of their energy by Earth's magnetic field. I don't know how long this would take, but it would be a very long time, as evinced that Mars has a much weaker magnetic field than Earth and yet still has some atmosphere. Meanwhile, particularly powerful solar flares could potentially generate electromagnetic pulses (EMPs) that could induce currents in and thereby damage electronics.