Taking the three refuges is just an expression of belief in
a) the Buddha’s achievement of nibbana,
b) a belief in the efficacy of the path he taught and
c) faith that some people(ariya-sangha*) achieved nibbana by using the path taught by the Buddha
(*as opposed to bhikkhu-sangha see below)
If you don’t believe those three things then that is fair enough.
But if you do believe those 3 statements, then you have in a sense already taken refuge in the Buddha, the Dhamma and the Sangha. The simple act of believing that the Buddha taught the cessation of suffering and a true valid efficacious path to that cessation, means that you have in a sense taken refuge the Buddha. Especially if you are actually practicing what he taught 
He said that long before His parinibbana as in sn22.43
dwell with yourselves as an island, with yourselves as a refuge, with no other refuge; with the Dhamma as an island, with the Dhamma as a refuge, with no other refuge. When you dwell with yourselves as an island, with yourselves as a refuge, with no other refuge; with the Dhamma as an island, with the Dhamma as a refuge, with no other refuge, the basis itself should be investigated thus: ‘From what are sorrow, lamentation, pain, displeasure, and despair born? How are they produced?’ sn22.43
I don’t see any conflict here. Ultimately, the path, is all about taking refuge in yourself and seeing the truth for yourself. We are all, as Buddhists, aiming for our own nibbana and our own direct understanding of the actual dhamma. Again, I see no conflict between that and taking the three refuges. Think about it.
The point is that by believing what He said, you have in a sense taken refuge in him. The refuge is about faith in the buddha’s nibbana and faith in the path he taught that leads to nibbana. If you really don’t believe the Buddha achieved cessation of suffering/nibbana/awakening and you really doubt the efficacy of the Buddha’s path/teaching, then no refuge. But, If you do believe those things and you are practicing the teaching, then you have already taken refuge in the Buddha and the dhamma.
Some people like to go through the ritual of taking refuge. It’s a beautiful thing, but it is not blind belief and it won’t make you enlightened.
Keeping in mind my points above. As we all know, or should know, unless we have our heads buried in the sand, there are plenty of bad monks and bad buddhists (and plenty of good monks and good buddhists). In that regard, the ‘political’ news posts on the watercooler are important to keep us, as a community, aware of what is going on. See here On Buddhist Religious Extremism
So taking refuge in the Buddha, the sangha and the dhamma are not mindless beliefs or mindless rituals (not for me anyway). They are in fact simply acknowledging that you believe the Buddha attained nibbana, you believe the buddha taught a true efficacious path to nibbana and that the sangha is a community of people that practised the path and achieved nibbana. That how I frame it anyway.
Note: Refuge in the bhikkhu-sangha seems to be the most problematic.
Disclaimer: absolutely no reification or objectification of any kind is intended this post.