One, if there are great, intuitive, affordable alternatives, they are not widely known.

Two, the downsides of Salesforce and Jira are at least well known and widely discussed. If you have an issue, probably somebody else has had the same issue, and a workaround may be known.

Three, "nobody got fired for choosing..." used to end with "IBM", now it ends with "SAP", "Salesforce", "git", "Quickbooks", or "Jira". None of them are so great, but they all work well enough to get the job done (since many reasonably successful companies use them).

I agree they aren't that great, though.