Partially yes. The problem with Flash ads is that they are difficult to block (without blocking Flash wholesale), because we don't have access to the runtime. There's no reasonable way for the browser to deep-inspect a Flash embed and determine whether or not it's abusive or relevant. There's also no way for your browser to alter and reformat content - it's either shown
precisely the way Flash wants it to be shown, or not at all.
HTML ads will be rendered by software the user actually owns and controls - the browser market is healthy, largely driven by open source, and there is choice in your "runtime". Making all ads render in HTML will be a tremendous win for the user.
As someone else mentioned also, Flash is one of the worst pieces of software known to man when it comes to bugs and exploits. Nary a day goes by without a serious 0-day Flash breach being discovered, and it is still notoriously crashy.