I didn't run into any of that in any of the companies I interviewed with; if anything, I found that coming in with a PhD resulted in correspondingly higher expectations. I'd treat any of the items you mentioned as warning signs and look for a better opportunity.
To specifically counteract the "can't code" item, have plenty of practical items on your resume; include your published papers and conference presentations, but also include projects you've contributed to and similar. (For people doing a PhD who plan to work in industry, make sure you present at some industry conferences, not just academic conferences, and publish your code as/into Open Source projects.) A CV for an academic position doesn't work unmodified as a professional resume (with possible exceptions if you want to work in an industry research lab).
In the specific context of CS, if you look at medium to large companies, you should already ask questions about the technical job ladder (such as making sure that one exists, rather than the only promotion path leading into management). Ask specific questions about how a PhD affects your starting position on that ladder. If it doesn't at all, then seriously consider looking for somewhere that it does. A company that values PhDs seems less likely to hold the misconceptions you mentioned.
To specifically counteract the "can't code" item, have plenty of practical items on your resume; include your published papers and conference presentations, but also include projects you've contributed to and similar. (For people doing a PhD who plan to work in industry, make sure you present at some industry conferences, not just academic conferences, and publish your code as/into Open Source projects.) A CV for an academic position doesn't work unmodified as a professional resume (with possible exceptions if you want to work in an industry research lab).
In the specific context of CS, if you look at medium to large companies, you should already ask questions about the technical job ladder (such as making sure that one exists, rather than the only promotion path leading into management). Ask specific questions about how a PhD affects your starting position on that ladder. If it doesn't at all, then seriously consider looking for somewhere that it does. A company that values PhDs seems less likely to hold the misconceptions you mentioned.