Me too.
The first instinct of a new player who was excited to try out the new concept of religions in Civ4 was to found as many as he could and build as many shrines as he could and spread the religions as much as he could. But more advanced players realised that it's often not worth the effort building more than 1-2 shrines or spreading more than 1-2 religions extensively. Now, isn't that counterintuitive? You are the first to research a tech and you found an awesome religion, you get a prophet and you can build an awesome shrine, but there is a catch? What the heck is this? This is broken!
Civ4 is a thinking game. If something doesn't work the way you think it does, it does not mean that feature is broken. Try changing the way you think. If you don't wish to do so, then go and play Command and Conquer and build 50 mammoth tanks as quickly as you can or something.
However, what you describe is an effective strategy. The effort put into spreading a religion generates a positive reward: it lets you build more religions buildings in your cities, and with a shrine it earns you 1 gold per city per religion per turn.
There may be
better uses for production than missionaries,
better uses for great person points than shrines, but the effort doesn't generate a
negative return on investment.
Corporations are generating a negative return on investment in many cases.
Things in Civ4 that generate negative returns on investment:
City growth past happy cap. It consumes 2 food and doesn't produce anything.
Extra cities with primitive economies. The maintenance costs go up, while the benefits don't.
The first of these two cases is a drastic improvement over previous versions of civ4, where your city would stop working if it got too large. The AI city governor is smart enough to avoid this, and you can convert these unhappy citizens into productive ones by generating more happiness in a number of ways.
The second is an explicit design decision to reduce the amount of management the game takes.
I don't see a reason that corporations need the same kind of punishment from being spread... Maybe at the higher difficulty levels it could be made to be questionable, but as it stands, it is pretty questionable even at Prince/Monarch.