It's a massive money laundering red flag, it's not at all surprising that Stripe doesn't want to deal with you.
Something can be perfectly fine for people to do, and it can be just as fine for Stripe to not want to handle it. They can choose what types of businesses they want to allow on their network. It potentially creates opportunities for other service providers.
Cash transactions above a specific dollar value literally generate reports to the government for investigation.
So, I think, yes, cash transactions tend to generate suspicion among anti-money laundering efforts.
The reporting you are referring to only relates to bank transactions. In the US, When a business deposits their cash receipts, the bank generates a report. There is no obligation on the business (e.g.a car dealership that sells a car for $100k in cash has no incremental reporting burden)
More importantly - because x can be used in the commission of y crime, but the vast majority of the use of x is in perfectly normal/legal use, one should not cast suspicion on the use of x or reverse the burden of proof on for using x.