Does the fact that it's used by large websites change the fact that it's a poorly designed language?
We tend to overvalue good design just for good design's sake.
You're completely correct, but at the same time, PHP also stands as a stark warning not to throw things together with no design, lest your misshapen child end up being immortalized.
PHP is simultaneously the best-case outcome and the worst-case outcome for a badly designed language.
A popular DB had an intentional feature that lost data on 32-bit builds. You might not get bitten until you've gotten plenty of data in it - it's still a terrible design that hurts everyone.