From the astonishingly prescient article, which was written shortly _before_ today's disaster:

The Achille’s Heel
...
But, there was a deeper, more fundamental problem that
Rutan wasn’t even aware of, one that has bedeviled the
program to this day.
...
Rutan steered away from liquid engines; he viewed them
as being overly complicated and possessing too many failure
modes. Instead, he developed a novel hybrid motor that used
nitrous oxide (laughing gas) to burn a large chunk of
rubber fuel. SpaceShipOne was the first time a hybrid
engine had been used in human spaceflight.
...
Rutan came out of SpaceShipOne’s short flight test program
believing the hybrid engine was simple and safe, and that
it could be easily scaled up for the much larger
SpaceShipTwo. He was wrong on both counts.

The first belief was shattered on a hot summer afternoon of
July 26, 2007. Scaled engineers were conducting a cold flow
of nitrous oxide that did not involve igniting any fuel.
Three seconds into the 15-second test the nitrous tank
burst, resulting in a massive explosion that destroyed the
test stand and killed three engineers. Three others were
injured.

Explosions are not unusual in engine development. However,
it is rare that anyone dies in them. Safety procedures call
for the evacuation of personnel to a safe area before any
tests begin. That was not done in this case; the dead and
injured were part of a group of 11 people standing near the
test stand.

Following the accident, Rutan and Scaled Composites claimed
ignorance. “The body of knowledge about nitrous oxide (N2O)
used as a rocket motor oxidizer did not indicate to us even
the possibility of such an event,” Scaled said in a press
release. The media and Scaled supporters have largely
parroted this explanation.

A team of experts experienced in working with nitrous oxide
reviewed the accident and disputed the claim. “This would
seem to indicate either a lack of due-diligence in
researching the hazards surrounding N2O (negligence) or a
wilful disregard of the truth,” they concluded.

Whatever Scaled’s culpability, there is no dispute the
accident delayed the program significantly. Work on
SpaceShipTwo was put on hold while engineers investigated
the cause of the explosion. Hybrid engine tests would be
delayed for nearly two years.

Once engine tests began again in April 2009, engineers
would discover that Rutan’s other assumption was wrong. The
hybrid engine just didn’t scale very well. The larger the
engine became, the more vibrations and oscillations it
produced. As engineers struggled to find a solution, Scaled
Composites and Virgin Galactic quietly began work on
alternative motor designs.

The failure of the hybrid to scale led to another problem.
SpaceShipTwo had already been designed and built. The
dimensions of the ship, the size of the passenger and crew
cabin, the center of gravity…all those were already set.
So, engineers now had to fit an engine within those
parameters that could still get the vehicle into space.

This is the reverse of how rocket planes are typically
designed. Engineers figure out the engine first and then
build the ship around what it can do. Rutan – a novice in
rocket propulsion who had hit a home run with SpaceShipOne
– got the process backward, resulting in years of delays.
This failure would cause numerous headaches.

The rubber hybrid engine did get a workout in three flight
tests, but the vibrations and oscillations it produced were
so severe the motor couldn’t be fired for more than 20
seconds. The engine was sufficient to get SpaceShipTwo
through the sound barrier, but it couldn’t get the vehicle
anywhere near space.

It was not until May 2014 – after spending nearly a decade
on the program, and a reported $150 million on engine
development – Virgin Galactic announced it would be
switching to a different type of hybrid engine, one powered
by nitrous oxide and plastic. They are hoping for much
better performance in flight.

By then, Rutan was gone, long since retired to a spread in
Idaho. It was for others to make the new engine work and
fix the mistake he had made.
...
Flush with success and not knowing what he didn’t know,
Rutan bet the future on a poor propulsion system that he
never took the time to fully test, much less understand.
His failure to grasp the nature of technology he selected
cost three men their lives.