documentclass{scrartcl}
usepackage{booktabs}
usepackage{pgfplotstable}
pgfplotstableset{
    every head row/.style={before row=toprule,after row=midrule},
    every last row/.style={after row=bottomrule}
}

begin{document}
begin{table}
    pgfplotstabletypeset[
    col sep=semicolon,string type,
    columns/col1/.style={column type=>{raggedright}p{.2textwidth}},
    columns/col2/.style={column type=>{raggedright}p{.2textwidth}},
    % columns/col2/.style={column type=p{.2textwidth}}
    ]
    {
        col1;col2
        long text with multiple lines;long text with multiple lines
    }
end{table}
end{document}

! Misplaced noalign.
midrule ->noalign
                {ifnum 0=`}fi @aboverulesep =aboverulesep global @...
l.20    }

I expect to see noalign only after the cr of
an alignment. Proceed, and I'll ignore this case.