Velocities can never be felt by anyone, only accelerations can. As such, only the thrust produced by the rocket engines can be responsible for anything the astronauts might 'feel'. For more information, I suggest you go through the 'Human tolerance of g-force' section in this link:
https://en.m.wikipedia.org/wiki/G-force
I assume you're only talking about the physical health effects during take-off, right? If not, then there can be some additional, often nasty side effects due to extended exposure to cosmic radiation, joint function decay from near 0 g's, and certain psychological implications due to being cut-off from regular human society leading to anxiety, depression and other effects [citation needed!].