ManofMan - I understand that in the specific situation you describe, Ryanair seems to be cheaper than Flybe. I do not dispute your argument from Manchester to Brussels on the dates you have chosen.
However, other consumers may wish to fly between other airports on other dates, and the prices difference between 2 or more airlines may be much much smaller. When the difference is smaller and one airline has a separate mandatory (but non-obvious) check-in fee it becomes much harder for consumers to compare the product offered by the 2 airlines and the price charged. Those posting on PPRuNe are likely to know much about air transport, but the general public are less familiar.
Transparency in business, particularly when focussed around retail consumers is a good thing. When products become harder to compare, we find that people increasingly fail to fully understand the products on offer, make the wrong decisions, buy a product that doesn't match what they actually want and overpay for it at the same time.