Encoding or decoding is not tokenization.
And the problem is probably more accurately stated as "be suspicious of any function implementing encoding or decoding" rather than focusing on the regex part. Use the correct standard function. Don't bash something together yourself. They're actually pretty easy functions to write if you know what you're doing, but it's even easier to use some tested already-existing function. In fact, it's so easy that the fact that you see someone bashing together a URL encoding or decoding function almost certainly proves that they don't know what they are doing, which in turn means the URL encoding or decoding function was written by someone who doesn't know what they are doing. Unsurprisingly, these are, well, to quote myself, "suspicious".
Yes, that logic applies to URL parsing as well! Unfortunately, browsers make URL parsing extra hard, which is really stupid, so you end up with more crap in Javascript than anywhere else. Even then you ought to prefer someone else's tested solution over just smashing out a regular expression; however, it is not a knock on the tested solution if it is a regular expression-based solution.