Your thoughts are secure. Mostly. For now at least....
From: The next hacking frontier: Your brain? - CNN.com
Some might question why anyone would want to hack into someone else's brain, but the researchers say there's a precedent for using computers to cause neurological harm. In November 2007 and March 2008, malicious programmers vandalized epilepsy support Web sites by putting up flashing animations, which caused seizures in some photo-sensitive patients.
From: The Journal of Neurosurgery, "Neurosecurity: security and privacy for neural devices", July, 2009
I agree with the authors that this isn't a significant issue now, but it will be in 10-20 years.Cognitive Function Augmentation
Another branch of neural engineering research rehabilitates cognitive function by using neural engineering to bridge damaged brain tissue; an example of this is memory augmentation. Several neurosecurity concerns may arise.... A hacker should not be able to alter the settings of the device wirelessly to stimulate the brain in an unsafe manner or to interfere with the normal formation of memories (integrity); for example, a hacker should not be able to cause disproportionately intense memories or cause unimportant things to become long-term memories. As noted above, the plasticity of the brain can cause spurious electrical signals to make long-term alterations to the brainís normal function.
Because these technologies will be intimately connected to a patientís cognitive functions, we must ensure that future technological advances do not unintentionally jeopardize the privacy of an individualís mind (confidentiality). For example, if it is possible to determine whether a patient is familiar with something by wirelessly eavesdropping on the implantís signals, then neurosecurity dictates that the implant should be designed to conceal this information; otherwise, the patient could be forced to reveal potentially private information. Last, we must ensure that a hacker cannot simply disable the device, thereby causing unexpected gaps in a patientís memory (availability).