From what I gathered that was actually a major reason, considering that the plan was to land the probe unharmed on the comet. More weight for power generation would likely have meant more weight to make whatever is involved in landing stronger and ultimately probably less weight dedicated to instruments.
https://www.orau.org/ptp/collection/Miscellaneous/pacemaker....
No, not really. They are pretty safe - you can hold one in your hand without a problem (barring a burn - they get hot).
A road accident would do nothing harmful at all.
> having it be stolen
That strikes me as pretty unlikely - they don't exactly drive on public roads.
There is absolutely a chance of fissile materials being stolen in transport - that's why there's multiple levels of security and multilateral treaties with most countries around the world about this kind of issue.
http://www.patriotnetdaily.com/wp-content/uploads/2015/11/Nu...
Plus, the kind of plutonium that goes into an RTG is fabulously expensive, not just because it doesn't occur in nature and has to be made via transmutation, but because it makes handling so much more complicated.
They'll have done the cost-benefit analysis and decided it simply wasn't worth it.
(Also, RTGs are big and heavy. New Horizons, which is a really small spacecraft, has a 50kg RTG. Philae only massed 21kg.)