'What does that mean for vaccines?'
It means he doesn't agree with your position.
He is not politically correct, he always says what he believes, he won't change his opinion for political expediency.
"CNN tried to destroy Donald Trump with vaccine autism question, but he gave this amazing response
...
Saying that he is in favor of vaccines in principle, he also explained, “But I want smaller doses over a longer period of time.”
Like a number of informed pediatricians and parents, Trump is very skeptical of the false promises made by the Centers for Disease Control and Prevention, as well as the vaccine industry that it promotes.
He even went on to tell a story about vaccines and autism:
Autism has become an epidemic… Because you take a baby in, and I’ve seen it, and I’ve seen it, and I had my children taken care of, over a long period of time, over a two or three year period of time, same exact amount, but you take this little beautiful baby, and you pump – I mean, it looks just like it’s meant for a horse, not for a child, and we’ve had so many instances, people that work for me, just the other day, two-years-old, two-and-a-half-years-old, a child, a beautiful child went to have the vaccine, and came back, and a week later got a tremendous fever, got very, very sick, now is autistic. …I’m in favor of vaccines [but] do them over a longer period of time, same amount, but just in little sections. I think you’re going to have – I think you’re going to see a big impact on autism.
Following Trump’s answer CNN turned to one of two actual physicians in the crowded Republican field – genius neurosurgeon Dr. Ben Carson – in an obvious attempt at convincing him to attack Trump for his stance. But while professing his overall faith in vaccines, Carson did say this: “We are probably giving way too many in too short a period of time…”
www.vaccines.news/2016-05-25-cnn-tried-to-destroy-donald-trump-with-vaccine-autism-question-but-he-gave-this-amazing-response-2.html
But I only know what I have seen of Trump. There may be lots more that he believes that will all come out when he takes over. We don't yet know what he will do and what he fully believes.