Using flexible SSL is a breach of user trust, as the traffic between Cloudflare and the host is not encrypted.
Yes, this is indeed true for the generic user level plans (free, pro).
Cloudflare did not lie about how the connection would be handled. In fact, they made it clear to those with sufficient technical knowledge via their control panel, help pages and blogs. So that is somewhat good.
Though what is disappointing is the fact that they have not outlined the con's of using flexible. The only con about the free cert options they had outlined is the system and browser compatibility when there is a lot more issues that are present under the hood that are not so obvious to the end users.
The only way you are going to get your own certificate used on CF is if you pay $200 or more. It is ridiculous.
EDIT: As pointed out in a post, Railgun may resolve the primary concern but this seems to start from the business plan also. So if that is not an option..
I had honestly used "Universal" SSL in the past. LetsEncrypt is a thing now so that would allow you to ditch CF right away if the server the site is hosted on supports SSL/TLS (user config), if you do not mind skipping the protection and caching, or/and if you do not want to pay for a certificate.
At the moment, I just use CF for DNS and redirects (for a domain I am migrating away from) only and it proves to be effective on that part. For my VPS, I use LE's certbot and crontab for obtaining certificates and for renewing them (automated) alongside Nginx and that proves to work very nicely. Got some near-perfect results in SSLLabs too (A+).
But yes, I strongly agree about using a server that allows you to use custom certificates when in production and handling user credentials and that flexible should be used for testing. Definitely upgrade when possible.