I work in the education / research sector. There's a reasonable amount of concern among the majority of people, as this is one of the few areas where we get out more than we put in. However, a short discussion with them usually lets them see pros and cons on both sides.
Scotland would have the second best university system in the world (scaled for size of population) but there are worries about research funding, the impact on fees / no fees, student numbers from south of the border, access to european funding, and specific worries in one or two sectors where Scotland takes substantially more than what would be a per-head share of funding in that area.
I don't think anyone believes the idea about continuing the pan-UK research arrangement (I know I don't, it'd be completely unworkable), so the lack of any clarity about what would be put in place means it's difficult to know what would happen. I usually point out a couple of things though
1. Typically the UK doesn't get its full return on European funding. European funding usually needs three EU countries involved in the bid. RUK universities would now be in a different country, which could make European funding easier to access, just by working with the same people you always have.
2. The opportunities to influence European funding increase by having a government lobbying for the specific research strengths of Scotland
3. Holyrood has consistently shown a more progressive approach to tertiary education than Westminster regardless of who is in power. This would continue in iScotland
In terms of other funding sources, I've heard of one charity (big life sciences one but I'm not going to name it - told in confidence) who have already confidentially told their staff that independence would make no difference whatsoever in their approach. However, you have to understand that research funding is all about the UK Research Councils. They account for the huge majority of University research funding and the detail on how other organisations would approach it is tinkering around the edges.