"The great rotation, the attractiveness of equities as a headline story, the macro environment (are) supportive in terms of selling equity," Chan said. "But in reality, whether it will materialize into actual returns nobody knows. For equities, it comes with volatility, market timing as well. Bonds still are a lower risk asset class," she noted. "We need to manage risk."
Others take a similar approach to their unpopularity, being upfront about the likelihood of losses.
Fixed income has done well for the last 30 years, noted Kumar Palghat, chief investment officer at fixed income specialist Kapstream Capital, which has around 6 billion Australian dollars, or around $5.33 billion, under management. "It can't go on forever," he told CNBC.
(Read more: Take cover! Bond market 'hell' could be on the way)
He doesn't have a problem with telling clients his offerings face a difficult outlook.
"They have to step up and admit that their asset class isn't going to do as well," he told CNBC. "They didn't do well in 2013 and they're not going to do well in 2014," he said.
"I don't sell the product just to sell it. I'm happy to say bonds will underperform equities. Otherwise, you're just pushing a product," Palghat said. He noted, however, that he continues to see demand from longer-term investors such as pension and superannuation funds which can't have all their money in equities.
(Read more: Euro zone bond rally may be ending: Here's why)
He tells his clients that if they must be in bonds, there are strategies to minimize the capital losses that are likely to come from the expectations interest rates will rise.
To be sure, being unpopular can be a boon for bargain-hunting.
As investors pulled out of emerging market bonds, Hamilton's Mongolia fund started buying, picking up Mongolian debt at around 58 cents on the dollar.
—By CNBC.Com's Leslie Shaffer; Follow her on Twitter @LeslieShaffer1