IMO the reason the protests made the front pages but the ferry disaster did not is simply that a) it didn't involve any/many Brits, and b) it's not an event of much ongoing significance.
Ships sink on occasion - especially elderly, first-generation Ro-Ro ferries, badly maintained and overloaded, as this one seems to have been. This isn't the first disaster of its kind, it certainly isn't the worst (over 4,000 died in a similar tragedy in the Phillippines a few years back), and it won't be the last. Moreover, as far as we know, there were no british passengers aboard. Once the enquiry's over, it'll be quietly forgotten about.
The protests over those cartoons of Muhammad, on the other hand, can be protrayed as part of an ongoing, escalating 'clash of civilisations.' they're closer to home, of much greater political significance, and are rooted in issues of religious difference, tolerance and values that in general are quite widely discussed these days.
It's not a matter of conspiracy, or some conscious decision to keep the ferry disaster off the front pages, and IMO it's not racism either: it's simply that people are more likely to get worked up about the protests than about a tragic, but not unusual, accident.