My spiritual adviser (a Taiwanese nun from the Chan lineage) told me that Buddhas and Bodhisattvas are not like gods or spirits, who desire only the most magnificent of spaces; that they are compassionate and all-wise, and in fact, have the least hesitation to go to the most terrible, detestable places to save beings. So, having an altar in your room is not at all offensive to them.
On the other hand,the Buddhas and Bodhisattvas will not punish you for breaking the Precepts; however, if you purposefully break the Precepts in front of an altar or Sutra (say, take intoxicants or commit sexual misconduct), the karma would be greater. IN an ordinary, mundane place (like a mall or gas stop restroom, for example) ordinary beings have no recollection of the Triple Gem; however, in front of an altar or temple, one's offenses will include not only the breaking of the Precepts, but also the act of ignoring the Buddhas and Bodhisattvas (in the form of their direct representations).
She summed it up this way: what you cannot do in front of yuor own mother or daughter, will you do it in front of the Buddha or sutras?
In the end, it's all about the spirit of respect. IF you can maintain mindfulness and respect because of a bedroom altar, then it should be no problem.
Thus have I been taught...