Section 1 allows reasonable limits to charter rights in a just and democratic society. "Closing the borders (period)" is not a reasonable limit, since it risks leaving people stateless and stranded in areas in which they are illegally.
The fact that there are "loads of potential charter violations" (are there, though?) will not allow the government to blatantly violate the charter in a way that would be immediately struck down by a federal judge, no. That's not how it works.
The Charter is not a suicide pact.
Evaluation of Charter breaches need to run through the Oakes test, to which I've applied my analysis, though I'm not a lawyer:
(a) is the violation prescribed by law? (here, in regulation, so yes)
(b) is the goal pressing and substantial? (yes, prevention of pandemic spread is both pressing and substantial)
The analysis then moves to a proportionality test:
(a) Is the alleged violation rationally connected to the purpose of the law? (here, yes: quarantine in a hotel for three days to await a test outcome to reduce spread of COVID due to idiots who refused to do so is entirely rationally connected to the purpose of reducing the spread of COVID)
(b) is the violation a minimal impairment of Charter rights in the context of the goal? Is the violation as small as possible, or within a range of reasonably supportable alternatives? (In my mind yes, it's minimally impairing: look at Hong Kong where you're required to quarantine in a hotel for 21 days and wear GPS wrist monitors, and other jurisdictions. Cost is an issue here, but it's minimally an issue. The point of that is to deter non-essential travel, which is in and of itself not unreasonable)
(c) Are the effects proportionate? Is the intended outcome proportionate to the violation? Is it a case of restricting free speech in the entire country so that, say, one business's operations in Saskatoon continue (random example)? (Here, I would say yes: it's on the higher end of infrignement but it is still entirely proportionate, given the element of discretionary travel that the person could freely choose not to engage in compared with the completely non-voluntary outcome of an innocent non-travelling person being infected by someone who absolutely needed to go to Cabo San Lucas in the middle of a pandemic)
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As to the amazing theory of "someone making a profit" - you people always seem to think that the government is making a profit off of COVID. Give it a year or two and then look at our income taxes - you will see that there is
absolutely no f----ing way the Government has made a profit here. The hotels are probably making some good money - but they've had no income since March, so this is probably a shovel full into a deep, deep pit. Also, the government has been renting this hotels since March 2020 - and providing places for people who have nowhere to quarantine before for free - so the imposition of a "pay your own stay now for your own vacation that you could have postponed like most other right-thinking people" fee is not unreasonable.
